Disney's Magical Express does not handle your bags at check out, unless you are riding the bus and ask them to store it under the bus for you. But there is no yellow tagging of the bags, no special Disney people that handle luggage when you are leaving to go back to the airport.
You can check in for your flight at the Resort Airline Check In desk at your resort. That is just like checking it in at the airport. You hand of your bags and they transport them to the airport. But just like checking in at the airport, there is no going back to your bags to grab something. They are checked in and gone. The next time you see them is at your home airport.