The way that restore works when you are recovering from a problem, be it a Virus, Spyware or a Application compatibility that causes your PC to go slow. Then having all your data files (i.e. letters, reports, photo, MP3s, Videos etc) on the second drive prevent them being overwritten when the hard drive is reformatted during the restore process.
So using windows explorer you should see the following layout:
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Note:
The C: and E: drives are the original drive and E: is the protected partition with the recovery files. While the local disks are the second drive with two partitions D: and F: allowing Business and Personal files.