I, too, like the Nook as a reader but am surprised at how weak the library management is (for sideloaded books). I've used a couple of different approaches that might be helpful.
First, don't overlook the value of Calibre's ability to create a catalog of your library. This catalog can be created as an ePub itself- which you can then sideload to the Nook and read like any other book. In my catalog, I have my books indexed by author, title, and series. This is entirely my preference- you can customize that pretty well. This option won't let you click items from the catalog and open them directly but it's easy enough to locate the book I want in the catalog, close the catalog, then select the book from the Nook's shelf.
The more recent solution I've also been using again is based on Calibre's capabilities. (Don't have Calibre? I can't recommend it highly enough!) I have Calibre configured with a plugboard to add the series name and number to the book's title when sending the book to my Nook. This is just another way to group my series and is pretty easy to set up. So I might send The Fellowship of the Ring to the Nook and the title would appear as "Lord of the Rings-01-The Fellowship of the Ring". Subsequent books in the series would group sequentially based on the series index number.
tl;dr - Calibre is a great solution with a variety of library management options.
Good luck and stop back in the Calibre section of these forums with questions!