You can find a file called KNOPPIX-CHEATCODES.TXT in the KNOPPIX directory of the Knoppix V6.2 CD. It has an interesting section
If you place an update*.zip or update*tar.gz file on the medium holding
the KNOPPIX data, it will be unpacked onto the overlayed filesystem
before starting "init", thus allowing quick reconfiguration of the
system.
I think you should save your customizations in a file update01.tar.gz using the tar program and place that file in the KNOPPIX directory before you burn your new DVD.