I think I figured it out.
I had to look at the Calibre library and import from the Nook as if it were a storage device. Now I have all my Nook items in my Calibre library, but now I have to get them to show up on the Nook in Calibre without having to duplicate them all on the Nook. Is there a way to flag as as being on the device without having to transfer them to the Nook where they already exist?