You haven't really given enough detail of what you are doing to give a proper answer. However using boot.ini you can make your computer boot from any bootable partition on any disk within the computer.
At the point that boot.ini is relevant in the start-up process the drive letter association (C or D) is not relevant.
For example, I recently took the hard disk (bootable Windows XP) out of my computer and put it into my wifes old PC along side the hard drive already in there (also bootable Windows XP). I simply changed boot.ini to include the information about the extra disk and the bootable partition and then at start-up the bootloader (well at least M$ half cocked version of a boot loader) displayed a menu asking which disk I wished to boot from.
NOTE: Changing boot.ini incorrectly can cause your disk (and hence your machine) to become unbootable be sure you know what you are doing before you do it. If possible make sure you have a method of recovery.
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