My Situation:

I have 2 hard drives; one is 160GB(slave) and one is 80GB(master). I have Windows XP 64-bit and 32-bit, and I was going to install Windows 7 beta just to try out.

What I Did:

1. I started with XP 64 on the 160, gave it the entire drive, and had it format it. I booted to it and got all my drivers working, migrated some of my data back from my external backup, installed all my programs again, and got everything working properly. I even messed with themes a bit.
2. Then I moved on to XP 32 which would get the first half of the 80; Windows 7 got the second half. Once I had both of those running I rebooted and tried to get back to XP 64, but it was not on the Windows 7 boot menu! So I went in and added it to the boot menu and rebooted again. It showed, and I proceeded. It failed. Again. And again. I was very sad. Unfortunately, the Windows XP 64 install disc I had did not have a recovery console so I couldn’t ‘fixboot’ or ‘fixmbr’ or anything at all. 
3. Something I’d forgotten about had been my downfall. Windows likes to install the boot sector to the master drive, even if you installed on a different drive. So, when I installed XP 32, it wrote over the XP 64 boot sector.

How To Do It Right:

Whenever dealing with installing Windows on a multi-drive system, always turn off the computer and unplug the drives you wont be using. That way Windows only has one place to install: the partition you choose.