Upgraded Outfittings for your ship are classified as General and Permanent. They can be accessed and installed/removed at the Harbor Master.
Permanent Outfittings are placed on your ship in the areas of Sails, Guns and Hull and cannot be removed and reused. If you remove them they are destroyed. They are placed into the slots on the right of the ship customization box and are installed in pairs.
General Outfittings come in many varieties (crew, sails, gins, powder, etc) and can be removed and placed on other ships if you desire. They are placed into one of the 3 slots along the bottom of your ship customization box.