Bonnie, I'm almost positive that the cave system at Cave's Branch is different than the one used at Jaguar Paw. But you could always email them to find out for sure. Even if it's not, like I mentioned before, the trip we did includes both tubing and cave exploration (rock climbing and stuff) and is much different than just the tubing. In fact, we talked to people at the lodge that did both and they liked the combo trip better.
I also thought of another trip that was suppose to be really cool. That's the Waterfall trip. Not sure of all the specifics. The guides really like this one.
All the trip leave at 9am. Whether you ferry it or fly to the mainland, the bus won't get you to the lodge in time. It makes a lot of stops between Belize City and Belmopan. Even the Express doesn't because it's schedule doesn't jive close enough with the ferry/flights. You'd either have to spend the night before at the lodge (bus it in) or have them pick you up wherever in Belize City like we did (we didn't want to spend a 3rd night off the island). The lodge transfer is considerably more expensive ($110 for as many people can fit in the van). Depends on how many people you have and what kind of accomodations you'd need at the lodge whether this would weigh out for you.
Hope this helps. You can email me at sharon_grajek@exe.com if you'd like more info "off line". Sharon