Burn it onto a CD first, or if you have the room, copy it onto the other drive, reformat, copy back, and reformat the second drive. If it's as gunked with spyware as you stay it wouldn't hurt that poor gateway drive.

thinking more about it, i would say reformat the gateway's drive (do you need your girlfriend's grandmother's porn collection?) and then install windows on it. Make it the main boot drive, stick drive number 2 in there, and delete the windows folder.