Put all ur BO skill points into beam attacks. I thought if i equiped all beam type weapons and they gave my 2 tactical BO beam over load 1 and 2 hoping i could just unleash hell by firing beam over load back to back. You cant beam over load attacks are on a timer from each other. So if u fire one you have to wait like 15 secs before u can fire the others.
it turns out its best to have a beam weapon, torpeode and a cannon and one phaser or turrent on the aft weapon. The having one attack for each style of weapon.
It seems BO's are all on the same timer, but Your skills and BOs are not. There is a short 'shared timer' but you dont have to wait the entire cooldown. I can use my own High Yield torpedo shot then about 8 seconds later use the one form my BO. (rather than the usual 30 seconds or so)
Every BO skill has an assoiciated ship system with it. If you look a the description of the skill you will see what system the skill uses. Each ship system has an associated cool down. Your beam overload I and II both use the Beam systems and thus using one will add a cooldown before you can use the other.