Going back to MCO, the Magical Express part is just the bus ride. Baggage and passenger check in is done by Resort Airline Check in, which is a separate service. You don't need to be riding the DME bus to take advantage of the RAC service.
That technical point out of the way, if you are using RAC to check your luggage you will need to call BAGS, the company that provides this service under contract to Disney, and pay any required baggage charges before you check in at the RAC desk. The RAC desks are not equipped to deal with the baggage charges. You will receive a package of information in your room the day before your departure that will explain the procedure.