you should still be able to take advantage of Magical Express, the service that transports you from the airport to your hotel. When you make your reservations, you can ask find out the number to contact them and make arrangements to have a spot on the bus from the airport. At this time, the service is free.
You should always know what airfare costs to book yourself to determine if you are getting a good deal. Also, many times when a tour operator books a package you may not be getting the ideal times or even non stop air travel between destinations.
I don't know what site you are using for booking, but you can simply contact Central Reservations for Disney and book your room, tickets and the free dining directly. You can probably ask them about air if they have it available to you. Where are you travelling from BTW?
