ok d00d. I found this while searching for stuff and couldn't figure it out myself.
I'm using 3.9

I started up knoppix, edited my menus.
then:
cp -Rp /home/knoppix/.config <path to remaster>/etc/skel/
chown -R root.root <path to remaster>/etc/skel/.config

then I want to:
<path to remaster>/etc/rc5.d/

and made a file called S99-Custom:
#!/bin/bash
cp -Rp /etc/skel/.config /home/knoppix/
chown -R knoppix.knoppix /home/knoppix/.config

rebuilt and it worked like a charm.
ymmv.