Caulker is cheaper for just about everything and most of the same tours, diving, etc are available from there. AC has more to offer in the way of hotel & restaurant choices, nightlife, amenities (Jet skis, parasailing, etc) Caulker is like AC used to be 20 years ago.
If you are splitting the trip up, why not spend part on the mainland rainforest and part on 1 of the cayes. It would be much more varied and a fuller experience of the country, than 2 islands 12 miles apart from each other. Or if you want 2 beach areas, how about 1 of the cayes and 1 of the southern shore areas like Placencia or Hopkins. Just some ideas on how to get the most (IMO) from a Belize trip!