The drive from Key Largo to Orlando Area is about 6-7 hours. Add another 1.5 - 2 hours to get to Crystal River. There's not much of anything to do topside in Crystal River.
If my best freind was asking me for advice, I'd tell her to make these 2 trips. Spend your time in the Keys, Miami, West Palm/Jupiter. Unless you have small children, forget the manatees. It's cool to dive there, but in my opinion is not worth all the driving you'll have to do. Better to save that for a trip where you are only going to do spring/manatee dives and combine that with Devil's Den/Ginnie Springs and maybe throw in a day of theme parks.