You can create a custom scan via the SEP interface to scan whatever you want.
Typically the AP will scan anything that is accessed, so if a user is placing files AP will scan it or if a user is accessing it.
Anything you download gets scanned etc...if the file is on the machine we have scanned it. The rest is left to the default weekly scanner.
I realize this isn't the best answer TomMLS though it is what it is.