I've shipped tires before through UPS. Not sure how Fedex wants to do it but I'd just call and ask.
All I had to do was wrap the tires in plastic bags and then tape around the tire so that the bags stayed on. Technically the bags don't even need to be there but I figured it might help to protect the tires and give you evidence of damage/tampering/gawking/fidgiting/whatever. The shipping label gets stuck on one of the spots where the tape crosses the tread. They (UPS at least) treat it as a large box with the dimensions of, in this case, 38"x38"x12".
I've never had a problem doing it this way.
Man, where's stuff like this when I have money? Wait...I never have money...