When installing another instance of W2k (or any other OS), always do so in a separate partition.
My first HD has 4 partitions, C with W2K for daily use, D with programs and data, E for download and F with another W2K for burning CDs etc.
The second HD has also 4 partitions, with G for the pagefile (fixed size, same file used by both W2K's), H for storage of program-sources, I for DriveImage images and J for my old Cobol programs (FAT16)