My laptop (Dell XPS)also has two drives (I added one). The master drive has all my applications installed, including Windows and Linux (it's a dual boot). However, all my data such as documents, photos, fonts, etc. are stored on the second drive. This way, if my operating system is ever infected I can format the drive and re-install without loss of data.
Windows 7 does have a method for creating a bootable recovery disk (DVD). While it's working, you might consider running the recommended anti- spyware/virus/junk apps, then creating that recovery disk.