so how safe is playing around with the drive letters?
I've never lost any data this way but you can get into some awkward situations when reassigning the boot volume, you may need to restart many times to get everything properly assigned.
how would i go about rearranging the drive letters, as when the 2nd HD is installed, i can't use windows?
The disk manager allows you to right click on a partition/drive and assign a drive letter. It's not clear to me why, but whenever a second drive is added, it is always inserted as the "D" drive initially, and it's a pain in the a$$!
I had planned to use a set up similar to yours for a backup system and abandoned the idea after many hours... My present setup is W2K w/NTFS and RedHat on a 20G drive, in different partitions. This has some partitioning limitations too and I'll detail them if you're interested. My second 20G drive simply serves as a backup. It's always cabled to the second IDE port as a master and I leave the power cable unplugged. Once a week, I plug it in and use Ghost to make a copy, then unplug power again. I may add a switch someday...
In your situation, perhaps putting W2K on one drive and Linux on the other would work. Simply power one drive down before powering the other up. It's not an elegant solution but it's simple, practical and reliable.