Copy as much as you can (documents, movies, videos, music) over to D drive.
Try to move as much as you can to D drive.
I think the drive was partitioned that way so that C drive would be specifically for program files and the Windows installation and D drive would be for all your other data.
Note: Do not move anything from C:\Program Files or C:\Documents and Settings\ (except items on Desktop)
If you really want to merge the two partitions, let us know.