I personally wouldn't bother with the built in back up ap. I have multiple hd's installed and none are partitioned. I have but one program that I put all the data (map software) to a slave. I also installed win 7 to a single partition using up the entire drive.
Regardless, if you are using a separate partition with which to use as your program files location, the built in ap will automatically want to back that up.
I use acronis true image home and it works flawless with my 11.2 gb of OS data which is stored as a disc image file compressed down to 5.9 gigs. Windows backup is slow, it creates multiple files, and it's compression sucks.
I'd just install clean to a non-partitioned drive if possible.