the codes are not interchangeable. Each airline has its own code even though both AA and AS run off Sabre. In your AS email and online when you look up the reservation it should also show the AA code by the AA flights. Thats the code you need to check in on AA. It doesnt always work seamlessly either when the first segment is AS and the second or third segment on AA. You would think it would and should but oddly isn't a very smooth checkin 70% of the time so it seems. At least thats my experience. I tend to get the please proceed to the AP to checkin messages or I get BP's with seats for the AE(maybe its an AE issue) flights that dont exist on AA Embraers like 2D 2F 6E etc....