I would put in the 2nd drive, format it, then if you want backup the c drive onto the d/e. Then start to copy stuff over etc, and if it breaks, you have your backup, and if not.. well you still have your backup.
Personally, I use 2 drives, 1 is 80gb raptor that is my C, and a 500gb standard for everything else. I only install stuff on the main drive, and everything else, movies, music, games, backup files all goes on the d drive. Then of course for super protection, I have a 500gb external that has a backup of all the stuff I do not want to lose on my 500 internal.
There are many ways to go about this. I would suggest going about it without trying to be too tricky as Window's does not like that.