If you run it from the cd then you would have to load up and install the atmel driver using your favorite method (ie. mounting hd, cdrom, floppy, etc..) The atmel driver should install onto your ram disk (directory should be similar) that knoppix uses. Hopefully you have enough ram to do so and set up the modules that way. The problem with this method is that you will always have to include a copy of the atmel driver and set it up every time that you run knoppix. I am hoping that one of these days that knoppix will integrate this driver into its autodetect scheme of things.

Until then good luck and let me know how it works out for you.