hi, my experience with disk cloning programs is that the default settings would try to detect your root directory and then ask if you indeed want to clone that drive. i suggest you try the cloning program and choose to store the cloned image files to dvds. and then test restoring the image on a new hard disk (if you have a spare hd). afterwards try to restore the dvd images.

this way, you'll be sure to know that the cloning and restoration works correctly. its indeed a weird case that your drive letters seem different and even interchanging depending on the active os.

i myself do not like the idea of dual/multi boot OS on the same hard drive. i prefer to manually set the boot option in the bios everytime i choose to boot from a different drive.

goodluck