I ran a short campaign set at sea and one of the things that made it short was that I was seriously overthinking the water aspect. I wanted it to be more realistic, with depth, decompression stops, etc. to make it feel less like "land combat but blue". I should have just stuck with the default rules or at most a very simple expansion of them.

When it comes to ship-to-ship combat, think carefully about how various abilities affect the dynamic. Boarding isn't much of an issue when you can teleport across, for example.

You can find a huge number of really crappy ship maps that are made for RPGs, but I suggest doing a bit of research to find a real ship plan and using that. It will feel much better for both sides of the screen.