Go to a shipwright and click on 'upgrade'. Then, get the upgrades you want to customize your ship.
NOTE- Only UNLIMITED access members can customize their ship, and only medium and warships can be customized.
TIPS- Before you customize your ship, get lots of gold to get multiple upgrades.To get gold, board public ships with very much loot and stay afk then when the captain ports, collect the gold!
Good luck on plunderin' with your new,customized ship!