NO, it is not in the atrium. You go to the actual arrival level on Side A and you will see a long corridor with rental cars, busses, etc. Just continue all the way down the corridor to your right until you get to the end of the hallway and see Disney. You can not miss it.
IT takes about an hour from the airport to your hotel. Usually 3 or 4 resorts share a bus. At peak times, there might be individual busses. They are all computer dispatched based on the number of ME customers coming in at any given hour. Sometimes there is a wait at the airport for your bus to arrive. Sometimes you sit on the bus for 20 minutes until you actually leave. All in all, count on about an hour.
If your room is not ready, you can just check in, leave everything you want with the desk, and go play in the parks. Your luggage will be delivered to your room and it will be sitting on your bed about two hours after you arrive. You do NOT need to be in your room for the luggage.
I did not notice if the busses were handicap assessible. I believe that they are not all that assessible. I work with patients in wheelchairs all day, and in all honesty, I kind of block that whole thing out when I am on vacation -- You should call and ask about that -- they might send a separate shuttle van for you. THe busses are the standard issue tourist-class busses used for tour groups - a steep and narrow three step entrance, a sharp turn to the left, and a step up into your seats. The wheelchair will fit if it is collapsible. It will not fit if it does not fold up -- but they might be able to put the chair underneath the bus with the luggage -- you should definately call Disney Reservations and inquire about that.