We got back from San Pedro, Ambergeris, this October. We also used Tradewinds for our condo. Nice location and unit, right on the beach (sea wall), close enough to walk to any where in town. One tip is that you can ask your housekeeper to do a wash and fold for you. Allows you to pack lighter and come back with clean clothes. When we asked what it would cost, she said "We could pay her what it was worth." She got the full US rate for that when we left. The four of us, two couples, really like Paradise Villas and Tradewinds.
To keep the kids shallow you will need to stay on the top of the reef. Not a problem since you can follow the bubbles of the group while they are deeper in the canyons. Besides, the top of the reef is where all the neat little critters live.
On our trip we used two dive shops, Ecologic and Island Divers. Doing it a second time, I would go with Island Divers.
One thing that really paid off for us was getting a 5 gallon jug of water rather than buying liters. The deposit on the jug was $12.5US and the water ran $0.60US a gallon. Got the $12.5 back when we left and it beat spending $1.50 a liter for water. Don't want the hassle of returning the jug, I am sure that the housekeeper will be more than happy to collect the deposit.
If you take a flight from Belize City to San Pedro, Tropic Air would get my business again. Talk with the ticket agents at the gate and see if you can get one of the kids a ride in the copilot's seat. It is open for passengers and something most people don't get to do.
Have a great time.