To keep boats, you need a place where they can be docked, which are marinas. Marinas are the only way to keep boats in game, which any character has. There is only one, Puerto Del Sol in La Puerta. You can buy it for 75 thousands (separate for each character). It's crucial if you want to keep any stolen yacht or buy any on-line.
The controlling itself is easy and similar to driving cars, so it shouldn't be problematic. In case of bigger boats, you may be problem with agility, so take it into consideration if you plan to sail through the narrow channels. Moving the left stick back and forward, you can also lower or rise the bow of your ship, what makes longer jumps possible. What is more, some smaller machines, like water scooters or submarine, may turn left and right quickly by pressing proper bumpers or L1/R1, depending on the console.