When my friend and I had our naval brikwars battle, we just put everything on a blue cloth, the one diver and one submarine was just considered to be underwater at all times unless we said otherwise. If rules are needed, I agree with IVhorseman on the marker idea, but instead of the stacks being one brick for one inch, I would suggest one brick for one story of height.
Ace, the glass table beats all others. It can support your battleship. You can put baseplates under and on it. And it can be as big as you want: Just go to Home Depot (or whatever) and buy some large plexiglass sheets, then use books or blocks or what not for the legs of the table. (If your battleship is that huge, then you should have lots of legs. I envy you if you've got a 20 pound battleship lol.)