You'll have to have an OS installed on D first, disconnect C (if it's a different physical drive) and check it will boot on D, then reformat C and do whatever you need to do then reinstall OS on C if that's your intention.
To boot a different partition (as opposed to a different DRIVE) you need to play around with your boot.ini file. Saying that, your boot.ini resides on the C: drive so when you wipe that... it will stop booting...
So, you need to change the Master Boot Record so that it looks at drive D:... Luckily there are other boot managers in the world that can do this such as LILO (Linux LOader) and GRUB.
I've heard GRUB is easier to configure and there appears to be a windows install version :