I'm starting now at UF COM, so I don't know if they are changing the procedure at all from last year. Your secondary will be sent to you via e-mail as an attached file (.doc). I applied kind of late, sending my primary app around middle of October and got the secondary within a month.
By the way, for whoever was asking about the average scores, the numbers that they showed us as a class during orientation was that the average GPA was a 3.78 (3.76 science) and the average MCAT was like 30.78 (these numbers are for the C/O 2007).
Hope everything goes well for you all.