Dos can only format a dos partition so that should be alright. But now that I am looking at the layout you have, dos/windows only expects one primary and the rest extended partition on the drive you have when installing and using the drive so I do not think it is going to work well if you try to install on a drive with 3 primary partitions. Your probably better off just putting in the spare drive you have as hda move the drive in there to hdb after having installed win98 to the hda boot with Knoppix CD mount the / partition of the knoppix install (sudo mount /dev/hdb? /mnt/hdb?) and edit the lilo.conf to change the root= to be for hdb? leave the boot=/dev/hda and uncomment the example at the bottom of the file for the other OS boot from /dev/hda1 then use sudo chroot /mnt/hdb?/ /sbin/lilo -v to write the lilo to the mbr of the win98 new drive and you will be able to boot both from that lilo screen and you have to change all the /dev/hda? entries in the /etc/fstab on the knoppix drive to /dev/hdb?. Replace the ? with the appropriate partition number(s).