Formatting winXP on 2 disk drives

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heres my problem, my family is computer illiterate, so naturally my computer is full of spy/adware, viruses and what not. I recently bought a new 120 gig hard drive, on top of my existing 40 gig hard drive. i want to store my current music files, web site files and general stuff i dont want to format on my new drive, and then reformat everything else. Can i formatt my computer without touching the new drive? will winXP pro allow me to choose which drive to formatt during the setup process?

Any info is greatly appreciated.
 
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