Windows won't allow you to change the drive letter of the system drive, BECAUSE, it would screw up everything. The only way you can safely change the drive letter (AFAIK) is to re-install.
If you have a network installed, you can MAYBE get round it like this:
First ensure that you don't have any drives with the letter C (eg,a CD/DVD) - if yo do, change them to a higher letter
Next enable sharing of the D drive
Open Explorer and choose Tools/Map Network Drive.
Select C as the letter to Use
Browse to the shared D drive in my network places (you can't just select the D drive from My Computer)
You should end up with C mapped to D. From then on any reference to mapped drive C (such as when backing up) should be re-routed to the physical drive D.
Can't test this properly, as (a) I already have a C drive, ad (b) I no longer have access to a W2000 machine, but it works in XP when mapping my physical D drive to another letter.