Out of the box, Calibre will not provide the type of organization on the device that you are looking for. You can modify the default folder structure to store books. See this section (
http://manual.calibre-ebook.com/gui.html#save-to-disk) and this section (
http://manual.calibre-ebook.com/temp...atelangcalibre) of the manual. This would allow you to group them differently. That would really only help you if you were navigating through the "My Documents" area on the Nook, not in the broad "Books" section, though.
Frankly, the Shelves function is the worst part of the Nook environment. I'm amazed that Barnes & Noble seems not to care.