Once you have selected the partition (with at least 4GB free) that you want to use to remaster the Knoppix CD, you need to make a directory structure to hold your remaster with the following command (the root of the partition I've selected is mounted at /share).

mkdir -p /share/knoppix_remaster/{source,master}/KNOPPIX

Now that you have your directory structure, you want to boot into the Knoppix live cd and copy the uncompressed filesystem into your directories. Once you have booted into the Knoppix live cd, mount the partition which on which you created your directory structure (mine mounts as /dev/hda4). After you have verified you have the correct parition mounted, copy the uncompressed filesystem over with the command

cp -Rp /KNOPPIX/* /mnt/hda4/knoppix_remaster/source/KNOPPIX

You also want to copy the boot and modules folders, the main html page for the CD and the other necessary files from the CD into your remaster directory with the following commands

cp -ar /cdrom/boot /mnt/hda4/knoppix_remaster/master/boot

cp -ar /cdrom/KNOPPIX/modules /mnt/hda4/knoppix_remaster/master/KNOPPIX

cp /cdrom/index.html /mnt/hda4/knoppix_remaster/master/

cd /cdrom && find . -size -10000k -type f -exec cp -p --parents '{}' /mnt/hda4/knoppix_remaster/master/ \;

Once all of the files are copied, your are ready to reboot back into your normal Linux environment.