If you're staying at Kelly's and diving with Aquanuts, you really won't have a say in the sites you visit. The captain decides based on conditions and the experience levels of the divers onboard. We dove with them for 4 days earlier this month and even with a group we had no say. Sites we visited that we liked were Spanish Anchor, the Benwood (also a good night dive), Woody's, Donut Hole, CIty of Washington, and the best were the Duane and the Spiegel Grove.
IF you can have the option, sign up for Captain Jorge's boat.
If you're doing both morning and afternoon dives, the shop is very disorganized and never once got the proper manifest to the boat. Make sure the tell the crew (more then once) that you're signed up for the afternoon. The office made a big deal about us initialing the dives we signed up for the day ahead, but they still never got the list right for the boat.
Also, the turnaround is pretty quick. Either have them call in your order to Hobo's from the boat, of stock up your fridge with sandwiches or other lunch stuff from Winn Dixie of Publix.
The boats can get full on the wknds (30-32 divers), but they do a good job of getting everyone into the water quickly. Changing tanks can get a little tight space wise. In the water, however, we were ofter alone and didn't see other divers until the last few minutes closer to the boat.
You mentioned the rooms. Absolutely book a specific room. Don't get a room with just one dbl bed, they are VERY small, no closet and no room to open bags (except on the bed) and no room for 2 adults to move around.
Have a great time!