I ran a pirates game with Skull & Bones, but ditched their ship combat rules which seemed confused and unfocused.
I had the PCs occupy different positions on the ship: The captain, mater of tops, master gunner, navigator, bosun, etc. all make skill checks appropriate to their position. The enemy ship makes similar checks (with circumstance bonuses based on speed, maneuverability, crew size and quality, and repair state of the opposing ships). Victory in the opposed rolls gives your ship advantageous firing position over the other: broadsides vs. aft, broadsides vs. fore/port quarter, etc.
Guns could be loaded with ball shot (does hull damage), chain shot (fired at the rigging, does speed damage), and grapeshot (targets enemy deck crew).