If you are working with a Travel Agent, she or he will be very helpful with helping you with your questions. As for flying into Ft. Lauderdale, we did the same thing, then took a free shuttle bus to our hotel, then the next morning took the free shuttle bus back to the ft. lauderdale airport, then hopped onto a coach bus to take us directly to the ship in Miami. I would definately recommend this option, the shuttle bus directly to the ship was arranged through our travel agent.....I believe it was a USA Coach bus. There was an additional fee for this round trip shuttle service, but very much well worth the $$$, we were dropped off right at the ship, and they got our luggage off the shuttle bus, and made sure it went right onto the ship which made things so much easier for us!!
In fact we are about to make the same arrangments again for a cruise we are taking in April. As I said, if you are working with a travel agent, she should be able to give you recommendations on hotels in ft. lauderdale that are cheap. I do know however, that you need to purchase those round trip transfers in advance, we purchased ours directly through our travel agent. Hope this helps!!
If you are not working with a travel agent, then I am not quite sure how you go about purchasing the shuttle transfer