As you first level up in the game you will notice the weapons and The consoles used to enhance the ships abilities have many different types. Here is what best to do if you want to keep the maximum best out of your ship.
Weapons come in several different styles. (For example; Phaser beam bank, Disruptor turret, Dual Heavy Poloron Cannons, etc..) The types are Phaser, Disruptor, Poloron, Plasma, etc.. The best thing you can do is mess with the different style's to fit the type of fighting style you are most comfortable with. But when it come's to the type's of weapon it is always best and recommended to stick with only one! For Example
I use a Advanced Heavy Escort Carrier With 4 fore weapon slots and 3 aft weapon slots. I would use my battle strategy keep to very front of the ship facing the enemy at ALL times. In the front slot's I would use Three Dual Heavy Phaser Cannons and 1 Photon Torpedo Launcher. In the rear or aft slot's I would use 3 Phaser Turrets. This allows me to pour ever weapon I got into the enemy at a constant barrage of attacks.
Now to the consoles. Consoles are a bit more difficult to master. But the only thing you can do really is to match them with you're main fighting style the weapons you use and you're ship's must valued subsystems based on your fighting style. Simple!
Bridge officer are the most important. Always set there abilities to match the fighting style and weapon's you choose to use. The bridge officer will always mean to difference between winning and losing a battle.