First. You cannot format your C: drive from within Windows, only via DOS. This is to protect your operating system, which the system believes will always be on C:
Second. I think you will find that your Boot.ini file is on C: This is the file that initiates the boot sequence and I think I am correct in saying is always written to C: So, if you format that drive, you have to save that file so that it can be replaced into the route of which ever drive becomes your C: drive. Remember also, the drive you boot from has to be made active. Do you know if that is the case with your present D: drive?