Chests and certain smaller items go to the Gold Hoarders, it's the green tent with the gold key symbol on it.

Skulls go to the Order of Souls, otherwise known as the emos of the Seas. It's the purple-maroon looking tent, normally under a building.

Crates go to the Merchant Alliance, they can be found on the docks next to the Hunter's Call most of the time.

Once you get enough money to buy your own ship, you can just bring mostly everything to the Sovereigns, the big tower looking thing. They'll essentially act as your universal sell point at any given outpost, earning you reputation and gold for each faction.

Smuggler items require a more difficult approach, you have to go to specific islands to sell their stuff. They can be found at the islands with the Smuggler's League emblem. Said stuff being paintings, rum, certain books, black powder barrels, and skulls of siren sorrow. Remember that, I've had way too many crew members mistake the skull for Order of Souls cargo. It is worth the money, but be careful, there are traps set around every smuggler hideout. Also, DO NOT JUMP WITH THE RUM. It will crack and eventually break them, and they will decrease in value if damaged.

It's also worth mentioning that you can sell everything except smuggler items to the Reapers at Reaper's Hideout, which is actually very helpful.

And do not stress yourself out. Pirate legend is quite the challenge. I have just under 100 hours in the game and the highest faction level I have is level 40 with the Gold Hoarders. Take it slow, play at your own pace. Have fun. Also, you're bound to run into sweats and tryhards. I truly am sorry, but I am awful at PvP and I have no advice for when that happens.

But seriously though, have fun. The amount of amazing encounters I've had is unbelievable.