...and you will know these things, grasshopper, once you have journeyed through this land.
I've just returned from Belize yesterday... My flight was 12:30 and I took the 7am boat from Caye Caulker... I was in the airport at 8:15am... so you shouldn't worry about losing your fligtht... The airport also is pretty small and if you do a web checking the day before you will have plenty of time.
I wouldn't spent a night in Belize city.
Good luck
Pablo

We found the taxis to leave about one half hour late, but we traveled Easter week and it was very crowded. If you can spend 2x the amt, take the plane. Less hassle and if you have large items they will not get abused. The water taxi IS the way most Belizians would travel to the islands, but you and your stuff gets rather jostled.
Also, only accept help from people wearing shirts with water taxi logos. Other people may want to "help" you but some of them will be thieves. Our only truly unpleasant experience in Belize was at the BC water taxi terminal with a dishonest "helper". (Vast majority of trip was wonderful, and we are considering a return visit)