You also need to find out if the taxes and port charges are figured into the prices you just found, sometimes thats the whole difference. Some travel agencies will buy up group space on certain sailings and offer the discount to you, it could be that you found some and the cruiseline didn't really drop their prices. Yes, you could have to pay a cancellation fee, so be sure to talk to your travel agent and find out all the details.
Yes, you can also purchase the transfers through the cruiseline even though you didn't book the air portion with them. Sometimes, you will find, its actually cheaper to just get a taxi at the airport to take you to the pier, something else to check out. If you are cruising on Grand out of Ft. Lauderdale, the taxi price is very reasonable, the port is right next to the airport, so its only about a 10 minute ride.
Enjoy your cruises, sure wish I had 2 booked