Yes, you can delete any partitions you want to while installing windows, although if you're using that as a D drive you'll need to manually format it to make it usable after you delete the partition. This can be done during the install as well.
The only caveat is that you want to make sure your system drive comes up as drive C, which you can accomplish by either installing windows with only the system drive physically installed, or by making sure that the system drive is on your lowest numbered SATA port.