To Disney, you should check in for your flight on line, when you do, you will be given the option to choose how many checked bags you will be bringing and you will be able to pay for them. If you attempt to pay at the airport, the cost is a tad more.
When you leave Disney, if you are driving yourself, check in online before you arrive at the airport (if you don't have a computer with you, guest services/concierge can assist you) and repeat the process. You can also use Resort Airline Checkin (RAC) to check your luggage. You will receive a packet the night before checkout with this process, but you will need to call a number for BAGS to pay for your checked bag fees. RAC has a specific process, so make sure you follow the instructions provided (ie. 3 hours before flight, hours of operation, ensuring you have enough time to have your luggage checked before 3 hours if there is a line, etc.).