Our transfers that came with the cruise were from the airport to the port and back to the airport. I called them and asked them how best to handle the transfers since we were already at WDW. They told me that I would need to get to one of the resorts where the cruise buses leave. For us the closes one was the Swan. We had to make our own arrangements to get to the Swan from the ASMu. From there we rode the bus to the port. They told me there would be an additional charge to return to a WDW resort from the port instead of the airport. The charge was $4 which they were able to charge to my credit card right over the phone.
If you are staying at one of the resorts where the cruise buses leave from, it should be easier for you. The resort will handle your luggage right from your room, as I understand it. Since we were not, we had to get our luggage to the Swan and check it in with the bell service people. From there we did not have to deal with luggage, as it was delivered to our stateroom for us. After the cruise, you have to pick up your luggage and take it through Customs yourself. (There are porters who will help.) Then you take it to the bus returning to the resorts and it is handled just like the Mears buses at the airport.