Here's some of the problems I ran into when I tried something along these lines......

1) I couldn't make a 100% flat battlefield for any battle. The game always made it slightly hilly. I could change the texture of the grass to water....but you don't get hills in water!

2) I couldn't restrict the unit choice so that the AI would actually use the right units in a water battle.

The rest is not actually all that difficult. You can have the ship primarily as missile troops, based on elephants ( in RTW ) with multiple catapults or ballista's replacing the troop models. Physical 'ramming' would result in sinking. I even skinned bits of the ship to the bones, so I could make it break and appear to sink when 'killed'. What spoilt it all was the fact that I could not control the battlefield as I needed.