Newbe--Ok lets try again on partition of HD for install

Ok.. let me layout my hardware AMD 3.2 board/win98se/dual 160G hd's(C: & D:)/
160G firewire HD(E:drive formatted FAT32)..1G DDR/dual dvd's
I want to use 100G of the E:(firewire) to setup partitions and install to.
fips.exe is on D: since my E: drive is not looked at to boot from but i still want to keep a
win partition, i've read the fips documentation and believe i can create another partition on
E:. However my thinking is I will still have to create a boot partition on C: where my boot
is. OR Can i make a boot CD for Knoppix and change my BIOS to look at the CD first and if there boot from it without distrubing my C:. In addition can the boot CD point to E: ?
If so would some of you mind to guide me along.

Thanks everyone
Michael :idea:

(in knoppix - kde) k button=> system=> qtparted => find your firewire device => partition 99.5 gb as ext2 or ext3, and 500 mb as linux-swap. Then, in konsole: sudo knoppix-installer
then choose the partition you want to install to, which is the one you just formatted, and install. Also make sure you install the bootload (LILO or GRUB) to your MBR. Then, reboot, and you should come to the bootloader. You can edit it in Knoppix to suit your needs.