My Google Reader contains a bunch of folders that all contain sites. When I import into NewsBlur, I have all of my folders, but no sites underneath those folders. The folders seem to contains stories from the sites, but no way to look at stories from just the individual sites.
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This is because of the site limit in the free version. I only had one site enabled under each of my folders because of the limit, so the folders didn’t show any sub-sites. I turned on sites within one folder and at that point the folder showed sub-sites. it looks like the answer is to either pay for the premium version or turn off/on sites that you want to see.