An important issue here is what drives will be seen?
If I have 2 drives with one partition on each drive, they will be lettered as C: and D: using the normal lettering scheme. Let's say, I install Win2K Pro on C:. Then I install Win2K Server on D: *without* disconnecting the drive that contains C:.
What I should see at boot is the boot loader with two options; Pro and Server. However, I will see both drives in *each* OS. \Program Files, \Winnt, and \Documents and Settings for Pro will be on C:, while those directories for Server will be on D:.
If I ever separate the drives, I don't think I will be able to boot into Server. If I am using C: itself, it won't be able to find the drive (D: ) where Server exists. D: won't boot by itself becasue the boot loader is on C:. *Maybe* repairing the Server install via CD is an option. I don't know for sure.
I probably wouldn't want to try to install Pro AND Server to the same \Winnt directory on any drive (C: nor D: in this case).
What would happen if you deactivate via BIOS one drive for install & operation (only C: is for Pro and only D: for Server)? I *think* the NT kernel will still see the other drive if it is powered and connected to the motherboard (yes, even though it is disabled in BIOS). This could wreak havoc on your lettering scheme (the disabled drive may still get a latter). Again, that could be a problem later if the drives are separated. On the other hand, if it works, you'll have a boot loader on each drive.
Clear as mud? If I had the time and resources, I'd try this little experiment.
-SUO