This has seriously become an issue for me, especially since I have multiple devices. I initially had an apple id that was linked to the itunes store with a primary email address which was @mac. I used this for all my App store/iTMS/MAS purchases. At some point came along mobile me which started using the @me version of the @mac email address to create a new apple id for me.
So now I have two apple IDs with the SAME primary email address. iCloud requires an email as an apple ID, which is a problem when trying to use services like Find my Friends or FaceTime, or GameCenter cause I can't use my original apple ID which is not an email.
To complicate things Apple seems like they want you to associate a particular email with a particular device. I guess this is needed for services like FaceTime and now iMessages.
This is all far too complicated for my liking. I wonder why they can't just merge the two IDs into one.
BTW, here's some documentation for others in the same boat.
Apple IDs and iCloud