If you had 2 partitions on your disk and a CD-ROM, your drive lettering would likely be:
C - The 1st partition.
D - The 2nd partition.
E - The CD-ROM.
If you booted the setup media and had setup delete the D partition, and install Windows 2000 to the unpartitioned space, at the conclusion of the setup process, you may find that the new Windows 2000 was installed to E and that the CD-ROM was now D.
When setup removes a partition, Windows 2000 re-letters all drives from that point onward.
To preserve the drive letters, exit the setup process after it creates the new partition and then restart setup.
You can also delete and recreate the partition using another OS instance, by using the Windows 2000 Recovery Console, or by using a seperatley bootable tool.
NOTE: If you had only 1 partition and had Windows 2000 setup delete it and install to the unpartitioned space, you may find that your CD-ROM is drive C.