I'm DMing a S&S homebrew campaign, homebrew story but using established lore. I've been using a combination of the Smoke and Sails and 2e Naval Combat rules. Smoke and Sails has more busywork for most of the party, but each action tends to have a pretty low impact like giving a +1 bonus to a different roll that can give a +1 circumstance bonus to one siege weapon attack.

I ended up hybridizing it with the Naval Combat rules, which is slightly closer to the PF2e vehicle and siege engine rules, but adds customization and upgrades on top of that, unfortunately as with pf2e vehicles, the pilot of the ship does most of the actual decisions and positioning.