Go hard at one of their SOL's and double board it, transfer all your men from one of the frigates to the captured SOL, retreat what's left of that frigate from the battle, then go after the 3rd SOL and take that as well.
Realistically you should be able to have 4 SOL's after mission 2.5 (1 from "fireworks", 3 from "treasure fleet") they are the hardest 2 naval missions in the whole campaign. once you have them, the game almost becomes too easy, even on very hard difficulty. You'll almost finish every mission capturing every ship and your hardest factor going forward is going to be upkeep. (as a rule of thumb always go straight for the biggest ship with 2 of yours, don't worry about what the other smaller ships are doing (by all means shoot them as you go past, but don't waste time and engage. Aim at the waterline and look to get lucky and blow them up). Once you have their biggest ship captured, the tables are significantly turned and you can clean up what's left of their fleet.
Another tip if you're finding your frigates don't have enough men to effectively control a captured SOL, is to have a transport with you full of infantry. Its risky cause troops are sitting ducks in the rowboat, but if you get them to the captured SOL you can instantly add 150+ men to the captured ship, even keeping your frigates fighting. Disembark them from the transport right at the onset of combat and get the transport out harms way (transport is too slow but them rowing is at 10 speed and much more manoeuvrable)
- When upgrading crew always go - morale -> rigging -> sea wolves. They offer percentage upgrades. The others that just boost stats don't matter later when your officers are trained up anyway.
-Cannon weight reduction modifications are your best friend for more crew and then I go the boarding mods. Also keep any long guns but look at downsizing any other guns/shifting to carronades to allow for more crew as well (standard guns weigh a lot, even by dropping the weight by 1 or 2 makes a big difference to crew numbers). Sell off your remaining naval guns from the admiralty tab and recoup and offset some of the money.