which is C or which is D is an artibrary decision of windows and can be FREELY changed from within windows (you just right click my computer, select manage, and change the drive letters to whatever you want).
There is no way for another OS to know which is which because they are not marked with a drive letter anywhere on the actual drive, it is just a decision being made EVERY TIME you load the OS (it trys to get the same names as before, but if the drives changed it will give them new names)
You can tell by the size which is which.
Also... are you sure you should be doing this? I mean, no offense, but you don't seem to actually know what you are doing... BUT, if you don't mind taking a little risks for the sake of learning, I will be glad to share any knowledge I have with you.
I think you should start by backing up your data in case you are messing something up and need to reinstall windows.
Anyways,which partition is FIRST, if you somehow installed into the second partition in the drive and it is not a boot partition, then maybe windows needs the data on drive D to boot (that would be a pretty botched install, but I can imagine windows doing that...)
Also, did you try running the online antivirus scan from
www.eset.com
It could end up removing a virus or more then one, and afterwards you would suddenly be able to format drive D from within windows. Which is the best solution.
Also, add remove programs ANYTHING that is on drive D... and try to just delete all the files on drive D to get a feel of what remains on it.