You can do it either online or over the phone.
I would make the reservation online. That way they will get your luggage if you have it. If you won't have checked luggage just go to the rental car level. They are outside and can make arrangements for you. Keep in mind that they stop every hotel for those with reservations on the bus.
Type "Disney's Magical Express" in Google. You can book online.
You hop on, I never made a reservation.
I think they run about every 30 minutes but call the resort for details
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