We did this last year and did Biscayne and Everglades. We stayed in Homestead and rented a car.
Day 1 was the Heritage of Biscayne morning boat tour and we also spent a little time at the visitor's center. The tour was excellent. They also offer kayaking and snorkeling, but this was January, and we thought it might be too chilly.
We stopped for lunch at Robert is Here and did the south part of the park that afternoon. We started at the Ernest Coe center and then drove down to Flamingo stopping off at the various boardwalks and paths. We ended that day with at evening ranger walk at Royal Palms.
Day 2 we made an early start as Shark Valley's parking lot can fill early. We picked up breakfast to have in the car and arrived at 8:00 on a day when they open at 9. We were about the 20th car in line. We explored the visitor's center, did the tram tour (which was excellent) and did the otter cave and bobcat walking trails. That afternoon we did an airboat tour with Rivers of Grass which I highly recommend.