Thelilgeek,
There is no setting in the PDO file but you can do it at the command line that calls pc-doctor with the PDO file, the switch is /pc:xx where xx is the number of passes you want.
The command line would look something like this:
PCDR.EXE /ba:3 /pc:10
This would load the overlay number 3 in pcdr.pdo and do 10 passes.
You could also add the /he switch to halt on errors as well as a bunch of others to save logs and control behavior. Read running PC-Doctor DOS from the DOS command line in chapter 5 of the PC-Doctor Service Center 6 Users guide. The File is: PCDrSC6_UserGuide.pdf on your CD-ROM.
-Fred