I'm writing this on 2 hours of sleep so bear with me, there will be spelling mistakes and I'll edit it when I wake up later lol. I've cleared i think 5 forts in total so this is what i've found. Anyway here's the guide.
Your first priority as you have probably found out if you have tried to fight ANY skeleton fort, is clear the cannon skellies that are hammering at your ship like me to my meat on a lonely saturday night. I wouldn't reccomend trying to solo forts unless you're a god with the Eye Of Reach but you'll typically need at least 2 people to clear the fort.
Find a spot at the fort where there's a gate that leads directly there, point your cannons at it even if you're still getting annihilated by cannonballs but that means your bud isnt doing his job correctly. This will come in handy later.
Baselines that should be said:
There are ammo crates that spawn around the island in several places.
There are powder kegs that spawn around the island in several places.
There are banana barrels and supply barrels that spawn around the island in several places.
Method 1: Easy
While parking the ship at the entrance, keep repairing ANY holes that pop up in your ship be it galleon or sloop.
If you are the cannon clearer, find the watchtower that has mr.skeltal inside of it that's shooting your ship and kill him. Good, 1 down, 1 to go. Go into the island whilst walking past the plethera of skellymen that are hungry for your booty. Find the cannon and 1 shot him with your blunderbuss. In my experience ALL cannon skellies are level 1 skellies (default no bandana) and are easy to kill. After both of the cannon boys are out, have your buddy keep his cannons aimed at the gait while you train all the skeletons in one big choo choo to the bone zone. Lead them all to the gate and have your friend rain hell on all of them with the cannons. You may have to spam bananas if a lot of blunderbuss skeletons spawn. Do this rinse and repeat until all skeletons are dead and eventually Jack Sparrow wants his compass back and do it to him too.
Method 2: Easier with bigger crews.
Have a dedicated cannon clearer (or 2) while the others repair holes. This time go to the main watchtower thingy that has the vault under it and place 1 Powder Keg in the center. You can have 1 person suicide to clear bigger waves if you cant get a shot in but most of the time it's pretty easy and you can clear it fast. Rinse and repeat until you're near the final wave.
Once you think you're about to hit the final wave, stack every remaining powder keg in the main room and you can 1 shot the captain and his crew. I think 3 does the trick. If everyone in your crew is in that room im pretty sure the captain and his main crew spawn in there bc thats how its been whenever i've done it idk i've only ran 5 forts so this is just based on what's happened to me. Whenever the captain spawns in the center, have someone shoot the powder keg and will cause a chain reaction instantly killing the captain, his crew, and any poor souls close enough to the kegs. If he doesnt spawn in there, train him into the room and then do it.
[EDIT] I forgot to mention that you ALWAYS want to keep 1 player behind on your ship watching out for other crews. I can not express how important this is. I've only been sank once by another crew while running forts and it's because i was a big ol' goof and we didnt leave someone behind.
Method 3: Challenge
So you've cleared close to 20 skeleton forts because you really, really enjoy PvE. Well bucko i've got a challenge for you! Sword and pistol only! That means NO powder kegs NO cannons and nothing else. The strat for this is pretty easy if you've played a LOT of CoD Zombies, it's how I've ran forts so fast. Just kite them around like you do in the cannon method but just shoot them with the pistol. Be careful though, you're not allowed to move powder kegs either, so watch out for any stray bullets. ;) You're only allowed 10 refills of ammo per person. After that it's sword only. Good luck! :D
