I would expect the PCs aren't going to be doing much adventuring on the boat, and that you're using it primarily as a method of getting them from Ice Chasm Place to Jungle Temple Land to Seedy City Ville. Because a boat which is small enough for a few PCs to crew it, isn't going to have much room for adventure on board, unless you take a few paying passengers and it always turns out one is a spy / changeling / homicidal loon / etc.

If you want something like "the Millenium Falcon vs TIE fighters" rather than "galleys or ships of the line, with hundreds of crew", then assign a few crew positions, maybe Gunnery, Shields, Engineering, Pilot, Damage Control. Add those skills to the game. A success by Engineering might buff Gunnery, Shields, or the Pilot's maneuvering speed--but someone has to choose where it's going. Gunnery might have to decide whether to shoot at the enemy ship or at incoming missiles. Shields might need to decide whether to divide power among all six shields evenly, or to strengthen some at the expense of others. The Pilot will have to decide how much power to put to evasive maneuvers and how much should go for straight speed. That way each person has something to do, and it requires decisions rather than just "Roll a d20. Roll a d20. Roll a d20. Roll a d20. Roll a d20. Roll a d20. Okay,you win."

Give the boat maybe 16 HP in each section (ie Gunnery, Shields etc) and have each hit apply d6 to its target area. Each section takes a penalty when reduced to 50% of HP.