I'm pretty sure as long as you have a reservation at one of the resorts (and have all the information for that reservation (person's name it's under, reservation #)) that you can use the Magical Express. I've never booked a flight through Disney, always on my own. Also, last time I went, the room was under my friend's name, not mine but I got the reservation # from her, called the ME number and got the transportation.
I also book my flights outside of Disney reservations. Call Disney back with your airline name, flight number, and arrival time. They will add Magical Express to your reservation. It is a great way to get from the airport to WDW.
If your staying in WDW resort and have paid just call them back for the Magical Express number and then call and give them your flight information and they will send you luggage tags (never enough so I ask for extras) We always book our own flights (not thru Disney)
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