Not sure I'm following what it is you're asking but if I were going to make a remaster of Knoppix from an existing hdd install I would just boot the Knoppix disc like normal- forget all that extra nonsense. After you boot, mount the drive you wish to remaster from and chroot to it. Then install OO. Don't forget to mount /proc first an unmount /proc before exiting chroot.

Is that what you wanted to know?