Craig, look at the "Active Sync" Properties in the Active Synch application.
From the main window of active synch, click "details".
Click Information type "files"
You will see some text stating:
"On this computer, synchronize files in this folder"
That is the location where files will get "synched" to the pocket pc device.
I believe there is a registry entry for this, so you could programatically change this to something more to your liking.
Regards, Gilbert.