First, note that "Drive C" and "Drive D" are Windows terms for partitions. In Linux, you'll see something like sda1 (the first partition on the first drive).
Please clarify the current configuration: It sounds like Linux is on the first partition and Windows is on the second. Also, can you always boot into Windows?
(You can see your configuration by booting from the Linux CD---open a terminal and enter "sudo fdisk -l". Post the results here.)
Note that boot code must be in the MBR of the drive---Assuming you only have one physical drive, then it must go there---not in "drive C" or "drvie D" which are really partitions.