If you computer is new enough, by using XP sp2 (you can go for sp3 now) you can call any logic drive any letter and install windows on any drive you like. Not just C. I've got two windows on C, D before!
So, if you want to keep the old windows system, you need to find programs like Ghost. If you have spare disk, backup to there along with all your other important files.
Then format the old disk, then ghost back your backup.
NOW, very important thing, was your windows installed on E or C? I've got a situation that my windows is crossing several logic drives, hence unless I got exactly same drive mapping (from C to H), the ghost back system doesn't work. It was W2K though.
Hence from then on, a clean system on C only is preferred, like others' saying.
I would suggest you reinstall the windows after you figure out which physical drive to be master and slave, and which physical drive is divided into how many/what logic drives.This is a much easier move and keep it like that from now on.
On PC can like to multiple physical drives, each physical drive can have up to 4 primary partitions with each become a logic drive with any letter you can assign to. You can have one primary and multiple secondary partition as well, but that is silly move for you can't just remove one logic drive.
What I do for all my 7 home computers (and 5 external HDDs) is to divide from 3 to 4 primary partitions on the main HDD. The first (assign to C drive) will be system only. The second (assign to D drive) will be data drive. The third one will be a backup drive to store ghost images.
If you want to swap contents on C, that is the windows system files, you can do whatever you want. Switching between XP/Vista/W2K etc.