If you choose "...to Root Partition" no harm will be done. Knoppix will be unbootable until you do something later. If your existing bootloader is same as this in Knoppix, you can simply take thing from Knoppix bootloader and put them in existing bootloader. Example:

title Debian GNU/Linux, kernel 2.6.11-kanotix-11
root (hd0,2)
kernel /boot/vmlinuz-2.6.11-kanotix-11 root=/dev/hda3 ro ramdisk_size=100000 lang=us apm=power-off nomce vga=0x317
initrd /boot/initrd.img-2.6.11-kanotix-11
boot

title MEPIS at hda1, kernel 2.6.10
kernel (hd0,0)/boot/vmlinuz-2.6.10 root=/dev/hda1 nomce quiet splash=verbose vga=791
initrd (hd0,0)/boot/initrd.splash

Here you can see 2 diferent distributions - one is original bootloader, and other is taken from partition and put here.