Their is no automatic way to do it you have to manually put books in shelves and sometimes they get lost if you keep books on the sd card.
I personally prefer using folders instead by using calibre send to device. Btw if you or your friend are even slightly into tech and don't mind rooting and stuff. I would recommend rooting and installing coolreader for non drm ebooks. It is a lot better than the Nook internal reader you will still need to use the nook reader for Library books.