thanks for the help. I'm doing all of these things already..and am just a bit frustrated I guess. I just had a sea battle against a pirate with 2 ships (I had 4). I had time to get 1 shot off before he had boarded me. :( Also, when boarded, I lose about 7 soldiers to his 1. :( I have it set on "easy" but I'm still getting massacred. :(
HereForTheBeer: Dunno about PR2, but in the first game it's fairly important to pay attention to which type of loadout you're using in the cannons. I usually started with chain shot to tear up the sails and get the speed advantage and then switched to either grapeshot or cannonballs, depending on whether I wanted to capture any given enemy ship or sink it. The AI is fairly aggressive on chain shot so be careful you don't end up slower than your opponent.
Another thing I would do is split up the crew fleetwide depending on the role a given ship would play. The small and nimble ships I used for harassment from a distance, to do as much damage as possible to the sails and crew; these would usually have less than the full complement of crew. The larger vessels I would give a full crew complement, to give them the best chance for boarding actions. Later, once you get your financial machine running full tilt, you can afford a full crew load on every vessel.
Don't ignore ammunition, either. Those heavily-armed ships go through ammo in a hurry, so don't pass up opportunities to buy more loads when you enter the larger ports. I don't think ammo counts against your cargo capacity (at least in the first game) so feel free to go crazy when you have the money. Nothing worse than running out of ammo mid-fight.
Hopefully the second game is close enough that this info helps. You said you're having no problems with the regular navy ships, so are you trying to capture any vessels to build up your fleet or sell for cash?