Great question, I'll be checking in late too and was wondering about the luggage.
How exactly does it work though, when you get the luggage yourself? Do you just have to wait for a later bus? I've not use ME before
We checked in pretty late ourselves when we went last year in May, and was also worried about our luggage, and no you don't have to wait for a later bus.

That late in the evening they are usually waiting on the people they know who will be coming in, or until the bus is full. And the good news about getting in so late, is that you won't really have that many people to deal with to check in!

Serious bonus!
I called in and asked one of the CM there at the POP what to do, and she suggested we not put our stickers on your luggage for ME to pick them up for you once your at the airport. The CM said that it would get to our room to late the next day (after a certain hour <I think it's 11:00 p.m.>they don't bring it to your room until the next morning and that can be as late as 10 a.m.)for us to be able to change and use all of what we would need for our day since we were hitting the ground running the following morning. She suggested we get our own luggage and bring it to our bus once off the plane and then take it to our rooms ourselves (there are carts that can be used to bring your luggage to the room).
Since you'll need to know where to find your luggage after your off the plane and then where to find ME, I suggest you get a Unofficial Disney Guide book for the lay out of the airport. Once you understand where your going to fly into gate wise and where your luggage will be you'll know exactly where to go once off the plane and then you'll know where to meet back up to, to get to check-in for ME.
You'll probably see the CM with the sign for ME, she will lead you to the area to check in for ME, be sure to have all your resort and ME information easily available, Disney sent everything <resort information, ticket information, and ME information>to use in a nice clear plastic envelope, I kept everything in there so I had it extremely handy when it came time to check in for ME and then also once at the resort.
Hope this was helpful, it's late and I've got a cold

so I hope this wasn't to all over the place. LOL If you have any more questions just ask, there's always someone to help.
