At the start of sequence 4, you get access to your hideout in Great Inagua. With this, you can apply various upgrade to it which are mostly for cosmetic effect.
Firstly, there are upgrades for the town
Harbourmaster - 500R - Unlocks shop
Tavern - 3,500R - Unlocks tavern
General store - 700R - Unlocks general store (guns etc)
Brothel - 15,000R - Allows you to hire dancers for free
Campfire - 7,000R - Let's you hire drunk pirates for free
Secondly, there are cosmetic upgrades to your villa (up near the viewpoint)
Facade - 6,000R
Tower and gardens - 18,000R
Guest house - 40,000R
I should stress that none of these are actually useful, so if you are short of money, spent it on your ship!
The best way to get money is from the Fleet Minigame, I'm currently bringing in at least 20,000R every (real) day. Another good source of money are the Royal Convoys or simply by plundering a lot of ships!