If she can climb the stairs for the Magical Express bus, the wheelchair can be stored underneath the bus with the bags.
You don't need to contact Magical Express if that is what you plan to do because you don't need a special bus.
If she will not be able to climb the stairs, you will need a lift bus. You don't HAVE to contact them ahead of time, but your wait for the bus may be shorter if you have arranged it ahead of time.
For the room, as was mentioned, you don't need to do anything unless you need an accessible room. If you need an accessible room with a roll in shower, call right now to the reservation number - that is a separate category to book and there are not that many of those rooms.
If you are in a resort without elevators, you will need to request first floor; that would be a request made by calling the reservation number.
The number you used to make your reservation is the one to call, not the resort number. Most of the resorts actually discourage faxes - they become an expense to the resort because of paper costs for printing and personnel costs to try to sort thru them and match them up to all the reservations. The DVC resorts have actually told members not to send them; they are not read and will be thrown out.
Otherwise, any room will work with a wheelchair and you don't need to do anything special.
The Skycap assistance that was mentioned is usually when the skycap brings a wheelchair for you to use and stays with you to push the wheelchair. You can request it from the airline, but don't count on it since you are bringing her own wheelchair. It might be provided if you have special situations- like more bags than you can handle with the wheelchair or not enough people to push a wheelchair and a stroller, for example.
If you need assistance from the baggage department to get to the Magical a Express bus, there are usually skycaps there offering services without having yo prearrange it.
But in general, wheelchair assistance is used for people who need to borrow a wheelchair for use in the airport.