Programs do not need to be on the same drive as the OS. You can install them anywhere. The installation program will write the necessary Registry entries to point windows to the system files. However should you need to reinstall your OS you will still have to reinstall the software since deleting windows deletes the registry file and windows has no Idea where any thing is without it. Your best option is if you do not have a hard copy (cd/dvd) save a copy of the Install shell to the Program drive in a back up folder this way if you need to format your Os HDD you can reinstall the program from your back up folder.
Edit: I just upgraded to a 250 gb SATA drive. Prior to this installation I had 3 HDD installed, a OS drive, a Program drive, and a back up drive. There were files everywhere. I installed the HDD's in my other computer and windows still found everything. I did luck out that the drive letters ended up the same and the OS drive originally came from that computer.
Edited by Sneakycyber, 03 February 2009 - 08:37 PM.