You can use the standard knoppix cd to boot from, if you have those files above, it will search the harddrive before the cdrom, and use those.
For what it's worth, on my system it appears that Knoppix tries the cdrom first. In fact, I'm running from the cdrom right now, even though the /knoppix directory is also on the hd. If I want to run Knoppix from the hd, the cdrom drive must be empty or contain something other than the bootable Knoppix CD.