As someone who had spent a fair amount of time in the Keys solely by being big-boat based, for your purposes I would definitely go the condo/skiff route. The funnest parts to explore are the shallow areas, and you get much more fishing options as well. We saw the big boat as simply being the mothership for the skiff, in our case a 13' Whaler.
Another option is to hire a guide for a day to get the lay of the area for both fishing and exploring.
There is a wealth of local knowledge information especially on fishing in the Florida forum of The Hull Truth.
Have a great time!
PS: I see you are from Atascadero. Where do you keep that boat? Morro Bay I take it?
"There's the Right Way, the Wrong Way, and what some guy says he's gotten away with"