It depends on your purpose: if you want to prove the distro isn't corrupted, dedicate one HD to Linux on a machine. No other HD's. Format it anyway you want. Let BearOps take over from there.
If you want to dual/multi-boot, keep the HD's the way they are. Check all the cables & jumpers. NOOOO cable select. Make sure they boot up in correct order: first HD1, 2nd HD2, etc. Or CD first. I would recommend using the entire 4.5G HD for Linux. It's more than enough. 2GB full install, usually.
Remove all partitions with DOS FDISK. Reboot as many times as necessary.
Format 4.5G HD with DOS FORMAT. No quick.
Boot to BearOps, choose custom/expert install. Select 4.5G and delete any partitions. Try Auto-partition, no luck? Manually make one giant 4.5G, mount point is /.
Install, write lilo to /dev/hdb, no numbering, write bootdisc.
Try bootdisc, if ok, boot to Linux and write lilo to MBR or /dev/hda.
My setup isn't too different from yours. Maxtor 40GB laid out like this: (3 primary & secondary)
good ol' lilo text boot screen
5g, fat32, w98
20mb, ext2, /boot (not used anymore)
3g, ufs, FreeBSD
3g, ntfs, empty
3g, ext2, linux, /dev/hda6
3g, ext2, linux, /dev/hda7
5g, fat32, w98 backup (ghosted)
5g, fat32, d:\games
10g, fat32, e:\my doc (all distros & storage)
It took me a few sleepless nights to set it all up. It's multi-booting fine. I use Partition Magic. The 20mb is in there before 8GB limit, in case, some old or weird distro requires /boot before the 1024 cylinder. Most recent distros don't need it. BTW, PM lets me MOVE the partitions back & forth. It takes time. No biggie for UDMA 100 & 7200rpm.