If you now have your HD's jumpered so that the windows drive is the boot drive, you will not be able to run your knoppix system because the lilo boot manager is not on the boot drive. You will have to install lilo onto the same drive as you are using as your boot drive.
You could use your Knoppix CD to boot into your knoppix HD install and try to edit lilo from there but that may be difficult because with the drive jumpers changed, the drive number designations may not be the same as what is in lilo.conf.
Perhaps the easiest solution is to reinstall knoppix but do the install with both HD's connected as there are going to be on the final system. Knoppix will then auto detect all partitions and include the windows option when it installs lilo. The HD install program should find the linux formatted HD & offer to install linux there. When prompted, put lilo on the MBR and it will install lilo to the mbr of the designated boot drive, ie the windows drive.