You can do it either way. If every block in the 9-patch is different (or even if every 9-patch is different), you get a very scrappy look.
I kind of like using a system. For example, every middle patch a dark red. That will be the small square in the quilt. I think it's also a good idea to use dark fabrics in the corners, light in the middle; just think it turns out nicer that way.
I'm not an expert on DP9, though!
Do a search here on DP9 and you will get lots of ideas. Also try a Google "images" search on DP9 -- there are tutes both here and online that will show how creating the 9-patch in a certain way affects the results in the quilt.