The exact same thing just happened to me. I booked my flight through United but it said "Operated by UsAirways...Check in at UsAirways counter". I called up my
AAA agent and asked her if I would still be able to use the resort airline check in, but she was unsure and told me that she would ask her supervisor and then get back to me. Well, I just got an e-mail yesterday stating that I
would be able to use the resort airline check-in because my flight was booked through United (even though it is operated by UsAirways)

. This whole code-sharing deal is really confusing though!
P.S. Disney's central office was no help in finding this information out. They were the first people I asked and this is what they told me:
"Well since it's operated by UsAirways, you are not eligible for Magical Express because UsAirways is not a participating airline".

I explained that I was and the only thing that was in question was the resort airline check-in and she told me to hold on. So I held....and held....and held...

then hung up. So I never got a definite answer. Then I was going to call the resort, but I wasn't sure if they would know. I didn't know who would know

. Of course, leave it to AAA to know. They always come through! (although I have to say, I won't actually believe it 100% until I am actually checking my bags and getting my airline tickets from the resort

)