Combat questions...

when you press "u" you open a window where you can assign bridge officers to their "stations"
when done you can use them in combat but some abilities only work when in range of a target and with a cooldown time

every ship has forward weapons and weapons which fire backwards
also on the "u" window you can put weapons to your ship
the top row are always the forward firing weapons while the rear weapons should be below the shield slot.

there are 2 major kinds of weapons... energy weapons (beams, cannons) and kinetic weapons (torpedos, mines)
energy weapons do good damage to shields while their damage to the hull is also relative good
kinetic weapons do only minimal damage to shields (almost none) but extreme damage to hull

-> problem is that you will need to get through the shields first before you can do damage to the hull
so you should focus on energy weapons.... you can take one torp with you to crack the hull at the right moment... or you do the entire work with beams or guns

if you have a cruiser then you should focus on beam arrays... the cruisers are relative slow and can not turn that good so you weapons which cover a large area
beam arrays can fire at 250° which has the effect that when you always keep the side of you ship facing to the enemy the forward and rear beams can fire at the same time since the arrays overlap their fire circles

if you use escort ships (which are faster than cruisers and turn better) you probably should focus on cannons or heavy cannons for the front weapons while you take turrets on the rear slots
cannons fire at 90° so you have to keep your enemy infront of you (which is possible since you can turn pretty good and fly better maneuvers), heavy cannons if i remember correct fire only at 45°
the turrets on your rear slots can fire at 360° so actually they always fire no matter how you turn your ship (and practically assist your forward guns)

the different fire angles of the weapons have a side effect on the damage of the weapons

while the 45° and 90° weapons deal the most damage, the turrets are the weakest
beam arrays are medium damage weapons

Important to know is that you can also mount tactical consoles on your ship which can boost your weapon damage.
e.g. You can mount a phaser relay that boosts your phaser damage (no matter if you use phaser beams or phaser cannons)
That phaser relay boosts only phaser damage... so using disruptor weapons next to your phasers is ineffective.
Focus on one weapon type and boost it with a console.
e.g. if you use phaser beams and a phaser relay which boosts all your 4 phaser weapons from a dps (damage per second) of 100 to 150 you will deal a total DPS of 600
but if you use 2 phaser beam, 2 disruptor beams and a phaser relay that boosts your damage then you got 2x150 DPS + 2x100DPS -> 500 DPS in total only
you would need to mount a tactical console that boosts disruptor damage aswell but that is also not effective
e.g. you take 2 phasers + 1 tactical phaser console and 2 disruptors + 1 tactical disruptor console you can get a total DSP of 600 (so far so good)
BUT
if you take 4 Phasers + 2 phaser relays you would get the bonus from the first phaser relay on all 4 phasers plus (dunno exactly) 75% bonus of the 2nd phaser relay
-> so for one weapon with 100DPS you might get from the first console 50dps and maybe 42dps from the 2nd console adding up to a total DPS of 192 for one phaser beam instead of 150 (for just one weapon boost)

(note the numbers here are totally random... pure examples)

There are also consoles which boost cannon damage only... but these consoles boost the damage for all cannons types (no matter if phaser, disruptor, tetryon etc.).
Thats looks good on the first view since this single console can boost all the different weapon types at the same time.
On the second view such consoles boost these weapons less good than the weapon type specific consoles.
-> a phaser relay mk xii (very rare purple version) can boost the phaser damage by max 30% (higher is not possible, except you mount more than just one phaser relay)
-> a console that generally boosts cannons (like the very rare (purple) mk xii prefire chamber) gives a max bonus of 20%

next question that might come to your mind: "what weapon type is the best"

The hardest question to answer... actually.
They all have their special advantages... some do more damage to shields... some to hull... some do extra critical damage... some can bypass shields... some damage subsystems
Here is a short description:

[extrabox]Phaser[/extrabox]

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[extrabox]Phaser damage is displayed as orange in color, or sometimes pale yellow. It is a directed energy primarily used by the Cardassian Union, the True Way Alliance, the Terran Empire, and the Federation. Starfleet uses phasers for both ground and space weaponry, although in-game any race or faction can use Phaser energy weapons. The term "phaser" is an acronym for Phased Energy Rectification. Player-acquired starships for the Federation by default come with Phaser energy weapons. Shields and armor with the [Pha] suffix modifier take 20% less Phaser damage than usual.[/extrabox]

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[extrabox]Energy bonus: 2.5% Chance: Disable 1 Subsystem for 5 seconds (Space) / 5% Chance: +2 Hold[/extrabox]

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[extrabox]Disruptor[/extrabox]

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[extrabox]Disruptors are a type of directed energy used in weapons, and are green or dark green in color. They are used by the Romulan Star Empire, the Klingon Empire, Gorn Hegemony, the Orion Syndicate, the Remans, and the Nausicaans. There are multiple types of Disruptor energy ranging from Type 1 to Type 3, although in-game there doesn't appear to be any difference between Disruptor energy weapons. Disruptors cause damage to the target by breaking the bonds of atoms. Shields and armor with the [Dis] suffix modifier take 20% less Disruptor damage than usual.[/extrabox]

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[extrabox]Energy bonus: 2.5% (Space) / 5% (Ground): -10% Damage Resistance Debuff[/extrabox]

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[extrabox]Plasma[/extrabox]

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[extrabox]Plasma energy beams are green/cyan in color. Plasma Beams are exclusively used by Borg and Vulcan vessels (Borg plasma weapons are green in color), while Plasma projectiles are used by the Borg, Undine, Romulans and Remans. High-yield Plasma projectiles are extremely powerful. Shields and armor with the [Pla] suffix modifier take 20% less Plasma damage than usual.[/extrabox]

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[extrabox]Energy bonus: 2.5% (Space) / 5% (Ground) Chance: Applies a non-stacking DoT[/extrabox]

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[extrabox]Tetryon[/extrabox]

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[extrabox]Tetryon energy beams are blue in color. Tetryon weapons are used heavily by the Hirogen and the Tholian Assembly, and they are available to anyone. Tetryons are subatomic particles that exist outside of normal space. When brought into normal space from subspace (artificially or naturally) they become highly unstable. Shields and armor with the [Tet] suffix modifier take 20% less Tetryon damage than usual.[/extrabox]

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[extrabox]Energy bonus:2.5% (Space) / 5% (Ground) Chance damage to Shields (Ground and Space)[/extrabox]

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[extrabox]Polaron[/extrabox]

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[extrabox]Polaron directed energy was heavily utilized by Jem'Hadar and Breen ships during the Dominion War. In Star Trek Online they are pink/purple in color and are available to all races and factions. They are first available to players at the Captain rank (Mk VIII). Polaron ground weaponry typically leaves an anticoagulant behind, although this isn't the case in the game. Shields and armor with the [Pol] suffix modifier take 20% less Polaron damage than usual.[/extrabox]

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[extrabox]Energy bonus: 2.5% Chance: -25 power to all Subsystems (Space) / 5% Chance: Weapons Malfunction for 5 sec (Ground)[/extrabox]

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[extrabox]Antiproton[/extrabox]

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[extrabox]Antiprotons, when confined into a beam, are normally crimson with a black void border
Antiproton/Phaser differences
Up close, the energy looks a lot more unstable, similar to Plasma and Tetryon energy. Antiproton beams were used by the Iconians, Undine, Crystalline Entity, and Fek'Ihri Horde (Undine antiproton weapons are pale yellow in color). In the game, Antiproton energy is used on end-game weaponry. Shields with the [Ap] suffix modifier take 20% less Antiproton damage than usual.[/extrabox]

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[extrabox]Energy Bonus: +20% critical severity (Ground and Space)[/extrabox]

Personally I have used phasers only so far as I started to focus on them when I still got free ships due to raising in lvls (and these ships had phasers mounted).
But in fact I am aiming to get antiproton weapons as the critical bonus does some extra DPS (it for sure matters if you do 6000 DPS on a critical hit instead of 5000 DPS)
However... antiproton weapons are ultra rare actually and extremly expensive
Infact I have not yet found out how to get mk xii antiproton ship weapons (purple quality).
Maybe I can get them after finishing tier 5 of the omega reputation project... the description is not that clear on that.

At this point it also needs to be mentioned that the above damage and weapon types can accour in special forms. There are hybrid weapons which are pretty rare.

e.g:

[extrabox]Polaron Beam[/extrabox]

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[extrabox]Energy Damage[/extrabox]

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[extrabox] 250' targeting arc
to target: __ Polaron Damage (__ DPS)
to self: -10 Weapon Power when firing other weapons
to target: 2.5% Chance: -25 All Current Power Levels [/extrabox]

vs.

[extrabox]Phased Polaron Beam (Dominion Polaron beam)[/extrabox]

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[extrabox]Energy Damage[/extrabox]

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[extrabox] 250' targeting arc
to target: __ Polaron Damage (__ DPS)
to self: -10 Weapon Power when firing other weapons
to target: 2.5% Chance: -25 All Current Power Levels
2.5% Chance -X to all shields
+2 Critical Chance [/extrabox]

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Hybrid weapons are generally more powerful as they combine the advantages of different weapon types.

Another thing worth to mention is that kinetic weapons like torps and mines have a shared cooldown.
So if you have 2 torps and fire one of them you will have to wait until that fired torp is ready again before you can fire the 2nd torp launcher.
Energy weapons dont have shared cooldowns... they simply fire when ready no matter of the status of the other arrays and banks.

Last but not least... also important is the damage resistance from weapons.

There are NPCs which have resistanced to specific weapon types. But that is not limited to NPCs only.
Engineering consoles can be used to raise the damage resistance in certain areas.

There are practically 3 forms of protection.

1. Hull plating which can give up to 40% resistance per console to kinetic damage (from torps, mines and explosions)

2. Alloys which give resistance to specific energy damage
-> here its neccessary to mention that there are consoles which protect from 2 damage types (e.g. phaser+disruptor or polaron+tetryon) and there are consoles which protect from 4 damage types (e.g. phaser+disruptor+polaron+tetryon)
So which one is better?
I would personally say "none".
The consoles which give protection for 2 damage types give max 40% protection against the 2 damage types.
The consoles which give protection for 4 damage types give max 26% protection against all 4 damage types.

Now lets imagine 2 examples.... first we take one console with phaser+disruptor damage resistance (40%) and a 2nd console that gives resistance to polaron+tetryon damage (40%).... that gives your ship a total resistance of 40% against these 4 damage types.
Now lets mount 2 consoles which project against 4 damage types at once (phaser+disruptor+polaron+tetryon). Each of the consoles has a 26% resistance to these damages types... so in theory 2x26=52. But thats not correct because when you mount 2 consoles of the same kind the effectivity gets reduced... and in the end you also will just have a 40% protection (just like with the first combination above).

3. There are alloys which protect from energy damage and kinetic damage at the same time.
It does not matter which energy... its a protection against all (6) energy types.
A protection against everything sounds great.... is great actually. Plus a kinetic protection.
There is just a slight problem... the max protection per console is limited to 20%

So make your choice. Wrong or right mostly depends on the choice of your enemy and his choice.

... just the basics

you dont have to train stuff,... other people with other skills can do the training for you or you can go to the boff skill trainer

however, you should focus on skills.
The chances that you are in a situation that your weapons which are maxed out dont do damage does not exist.
The chance that your phasers do less damage against klingons is very likely. But practically against all others they work perfectly. You always have the chance to choose who you will fight and who you better avoid.

Here is just an example (no real values actually):
assuming you have 8 phasers with a base damage of 100 and 2 phaser relays which together give you a bonus of 45% damage you will end with 8x145=1160 damage

now lets assume you use 4 phasers with one phaser relay 30% bonus and 4 polaron beams with a console which gives you 30% bonus to polaron damage
so we have 4x130=520 damage on phasers plus 4x130=520 damage on polaron beams -> total damage = 1040

While both examples use 8 weapon slots and 2 tactical slots the example with the focus on one weapon type clearly does more damage.
Why do 2 phaser relays only give 45% bonus while 1 relay in the 2nd example gives already 30% bonus?
-> coz these consoles stack and the 2nd console always grants less bonus (mostly just 50% of the first console)
Still its 10% more effective in this example to focus on one weapon type... and even if your enemy as a 10% resistence (which is very likely) then you would still do the same damage that your mixed weapon setup does.

Just dont focus on plasma weapons. Most elite shields grant 20% plasma resistence