Before going to war with Spain try taking awhile to build up your navies massively, especially where he has ships concentrated, and then pounce by land and sea at the same time. If you have sufficient naval superiority you should be able to mop up most of his ships in just a few turns, leaving you with mastery of the seas.
Naval combat isn't one of the most exciting features of the game, but it's one where it pays to plan ahead.
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