In this, I was inspired by the historical flota, the annual treasure convoy sent from the New World to Spain. Accordingly, I put all my Spanish ships on one side, and during the game had them move fairly mechanically across the board in a group.
I didn't make up formal rules for this, but just controlled their movements as a sort of gamemaster for the scenario. At the same time, we each ran a small squadron of English and Pirate ships, intent on disabling and boarding the Spanish Galleons, each of which was carrying a random selection of treasure.
Here's my own squadron of English Sea Dogs moving in. I made the islands out of styrofoam, cut with a styrofoam cutter, and covered in resin pumice for texture before painting. I was inspired by the awesome Pirates of the Spanish Main scenery over at the Shifting Lands website.
Losses among the flota were heavy.
A pirate squadron can be seen at the top of this picture. In the foreground, the English squadron has already disabled and pillaged a medium-sized galleon. Unfortunately for the English, the mighty Spanish flagship Guarantor is just moving into position between the sand bars. Next turn it started blasting the smaller English ships out of the water.
My niece won with the most gold at the end of the game. I lost, with only one ship still seaworthy, and little gold!