Slincoln,
Saving the overlays in a session does not modify the image on the USB key in any way, It just changes the pcdr.pdo file in the ram drive.
To make changes permanent is a multi step process.
1) Modify the overlays to your satisfaction.
2) Exit to DOS.
3) Copy the pcdr.pdo file from the ram drive to the USB device.
4) Remove the USB device and place it in a workstation with WinZip (or equivalent)installed.
5) Open up the PC-Doctor zip file, e.g. DS301590.ZIP for Service Center 6
6) Place your modified PCDR.PDO file in the zip file and save.
You will then have your own customized PDO in the build on your USB key.
-Fred
P.S. This procedure is also valid for any other files you wish to modify like INI settings. If you gum up the works the USB Key restore tool will put it all back to stock.