I think it helps tremendously if your kids are not hooked on handheld video games and DVD players. If you can keep those off the boat and concentrate on the boat handling, the sealife, the view as well as the various 'at anchor' pastimes at the end of those short hops they should have a blast. If they enjoy books that's good for the slow/quiet times.
Beachcombing, swimming in warm water, dinghying around, exploring new towns and cultures should be plenty to keep them amused and interested.
Sounds like a great trip! and 2 whole weeks!!
".. there is much you could do at sea with common sense.. and very little you could do without it.."
Capt G E Ericson (from "The Cruel Sea" by Nicholas Monsarrat)
1984 Fast/Nicholson 345 "FastForward"