BOAC,
I think you will find that W2K is booted from the C: drive, insofar as there will be some files (from memory, possibly boot.ini, ntloader.dat or some such) that are on the C: drive, even though the system files are on the D: drive.
Win NT (from 3.xx on) always had the separation between the boot disk and the system disk - although IIRC the system disk is where the boot files are and the boot disk is where the system files are. MS, eh? Clear?
On single-disk systems this usually doesn't matter, but with multi-disk systems it does, as you are finding out.
There are 3 steps involved in getting a bootable O/S on a hard disk:
1) Get the hardware recognised by the BIOS - jumper setting
2) Create a partition for the operation that is recognised as bootable by the BIOS - fdisk or similar
3) install the operating system
Steps 2 and 3 are often combined, so it isn't always clear. So my belief is that making D: the primary master will not work. You will also need to make it bootable.
I have done something like you want to do - with a SCSI based system - and what I suggest you do is to back up your data, export your identities and start over from scratch with a clean install. It gets very messy.
An alternative is to get hold of Norton Ghost, or similar, which will create a (bootable) copy of your existing C: drive and allow you to re-create it on your new 20GB disk.
Good luck
SD