It all goes for style of play. Merging is the way to go if your not going to retrain. Since I retrain I merge until the ship has too low of a number that it can no longer merge w/o being lost. If I'm far from a port I will merge ships together as there is little hope in getting them back safely.

In your example you have 3 ships with 20 men. Heres a little on naval battles, if you go up against a 1 ship with 50 men you have increases chance of losing as those 50 men can take out 1 ship at a time. but 60 against 50 would put the day in your favour. At least from my experience it seem to take unit sizes into account. That is also why biremes get torn up later in the game because they are going up against bigger ships but there exp keeps them alive.