All custom configuration for the knoppix user comes from /etc/skel so copy any changes you make from /home/knoppix to /etc/skel. Specifically ~/.kde and ~/.kderc would most likely be needed for any customization related to kde. To make this simple I ususally use a basic script something like:
Code:
mv /etc/skel/.kde /etc/skel/.kde_old
cp /home/knoppix/.kde /etc/skel
mv /etc/skel/.kde /etc/skel/.kderc /etc/skel/.kderc_old
cp /home/knoppix/.kderc /etc/skel
This way you can make changes to kde and run your script to put those changes where they need be. Then you can test it out without rebooting like so:
rm -rf /home/knoppix/* .*
init 3
init 5

That will restart KDE (or whatever desktop you booted with) with the new configuration from /etc/skel. This of course works if you are booted directly into your remastering environment. If you still use chroot then I do not know.........