There are two scripts that control how Knoppix is booted: linuxrc and 45xsession.
linuxrc: Knoppix loads the kernel and mini root partition from /KNOPPIX-CD-ROOT/boot/isolinux. If you use the 2.4 kernel on knoppix then the kernel loaded is linux24 and the mini root is minirt24.gz. If you use the 2.6 kernel on knoppix then the kernel loaded is linux26 and the mini root is minirt26.gz. You can view the mini root by copying it to another location, unziping it, and loop mounting it.
Code:
cd $HOME
cp /KNOPPIX-CD-ROOT/boot/isolinux/minirt24.gz ./
mkdir foobar
gunzip minirt24.gz
sudo mount -t ext2 -o loop minirt24 ./foobar
Inside the minirt you will find a executable script named linuxrc. This linuxrc script is init script for Knoppix and controls many of the bootime cheat codes.

45xsession: This script lets Knoppix figure out how to manage the knoppix user's home directory, starting X, and other cheat codes. See my HOWTO http://www.knoppix.net/forum/viewtopic.php?t=13867 where I edit the 45xession file in order to correctly populate the /home/knoppix directory.

I hope this helps.
James