What if you have a stack of different ships, some fast and weak (Barques), some slow and powerful (Caravel)? I have a stack of 2 caravels and 2 barques guarding the english channel lead by a 4* caravel to make sure it's secure.

Likewise I have a similar force guarding the straights of gibraltar as it's a choke point, but my enemies just sail on through without fighting and my fleets can't stop them. The only thing I can think of would be to make up a stack of Barques and leave them guaring choke points, but then I'm wary that a single strong but slow ship will wipe the lot of them out (as I have seen happen)

also, what determines how far they can move in one turn on the map? My caravels can move multiple teritories, but the "faster" barques can only move one?

I think this aspect of the game is one of the few areas of improvement that exists.