Don't Forget About Calibre's Ability to Create a Catalog
I have been on the Nook platform (STR and NT) for some time after switching from Sony Readers. After the switch, the only thing I missed about the Sony Readers was the ability to create collections with the series as tags. I also am perplexed at what the rationale was in the oh-so-limited functionality of the Nook Shelves feature.
BUT- I stumbled onto Calibre's ability to create a Catalog in ebook format listing the contents of my collection. This absolutely provides better flexibility in how I manage my books on the device. The downside is that the catalog is a separate ebook and you can't select books from within the catalog but I can live with that.
Try creating a catalog (under the Convert Books button). You may be happy with the result!