The easiest way to backup and restore Fences settings is via the snapshot system. Simply copy the snapshots from one machine to the other, then restore the snapshot via Configure Fences -> Tools -> Snapshots -> Restore Snapshot. Snapshots are stored in the following directories:

XP: C:\Documents and Settings\USERNAME\Application Data\Stardock\Fences\Backups
Vista/7: C:\Users\USERNAME\AppData\Roaming\Stardock\Fences\Backups

You will need to replace USERNAME with your user account name on your PC.

Alternatively, you can import the following registry key into the new machine's registry:
HKEY_CURRENT_USER\Software\Stardock\Fences

Fences cannot be on top of Windows; it is desktop only.