Here are some guidelines as naval warfare in MTW is sorta random.

1) never launch a naval assault in the same round as you score a major land victory. In these situations a single enemy ship can wipe half your fleet in that sea region off the map.
2) if you have 2 ships versus an enemy's one ship, send in your ships singly to attack, but send them both. This gives you 2 chances to stop the enemy ship. If you have 4 ships versus your foe's two ships, send them in two stacks of two. If your fleets are about even, send the stack.
3) evaluate an enemy vessel's speed. If it's speed is higher than your pursuit ships, it stands a better chance of evading you.
4) in naval combat, valour counts.