Unfortunately, while Calibre's library management on your PC can't be beat, Calibre can't really help on the Nook device itself. (That is a limitation of the Nook environment- not Calibre's.) Take a look at this FAQ:
http://manual.calibre-ebook.com/faq....es-on-the-nook
The one piece of good news is that all books on the Nook STR show up under "Books" in the library. B&N purchased content and sideloaded books- all appear in the same place. The ugly part is the Nook's Shelves functionality. You have to individually add books to each created Shelf. You could certainly create a Shelf for "Mystery" but then would have to individually add each book to that Shelf from the library interface on the Nook. It is a slow, cumbersome process.
Definitely take a look at the Catalog functionality of Calibre. (
http://manual.calibre-ebook.com/catalogs.html) This allows you to create a new ebook catalog of your library. This new book can be loaded onto your device and read there. You could have your Catalog cross-reference books based on genre. That is a decent workaround for the Nook's subpar method of grouping books on the device.
Good luck!