If you reboot your computer then the search results will be lost and you will have to run the scan again. (When we release version 4 of Recover My Files in December 06 you will have the option to save search results).
Probably the only way to avoid this is to connect the second drive using a USB case.
You can make your own CD if you wish. There are instructions located here:
http://www.recovermyfiles.com/data-recovery-cd.php