Tempe's intention is for them to be automatic, but my own experience has been inconsistent:

Automatic e-mail upgrade notification at my window (East)
Automatic e-mail notification that I was waitlisted at my window (East)
Augomatic e-mail upgrade notification one day after my window opened (East)
No e-mail upgrade notification (East & West)

Hopefully once the reservation systems are fully merged we will consistently receive notifications whether or not we have been upgraded. It would just be nice to know what to expect.