Manual battles obviously.
Best fleet combo I've found is three large warships (the ones with the 2 chevrons), and two small warships. The three larger ships are interchangeable but the two small ones should be the frigates, the fire arrows and reload is pretty help full. There is also the grenade which is on the gallon i don't recommend this one because of the splash damage can cause friendly fire.
Use canister shot to lower their crew, fire arrows to hold ships in place and reload on troublesome ships with large crews. Also use heavily damaged ships to capture since the AI usually diverts its' attention from them once they are locked in capture. You may still lose a ship here and there but not constantly.