Our approach to naval combat - let player do whatever they want with ships. Task any units on the ship and they`ll board it - as many as will fit. Any units other than Dragons and Ogres. Note that really packing the ship with units will slow it down.
Some interesting ideas:
-Get a trebuchet, some archers, and melee units for well rounded all uprpose ship.
-Pack it up only with melee units for a great boarding ship, if your looking to capture some enemy ships.
-Only archers for a great ship-killing vessel.
-Put only a few units on the ship, to get a really fast moving scouting vessel.
-Pack ship with only trebuchets and catapults - to get yourself something like AoE3 bombard galion
-Or even pack the ship full of cows and peasants, and make a floating farm
Here`s a screenshot of a ship I packed with 15 archers, 20 swordsman, 1 trebuchet, a hero, and a few cows for good eating later, 'where`s the rum?'