Ok...well re. Calibre and sideloaded ePubs and images on cover flow...I have found several things.
1. When you let Calibre sideload a book it will place the book in the root directory as a directory of the Author and inside that directory is the ePub and an image file (jpg) for the cover (if you either downloaded one in Calibre or made your own).
2. The problem is IF that directory doesn't live in the 'My File/Books/" directory the Nook cannot resolve the image. It will find the book but you won't get the cover.
My workaround is to continue to use Calibre to convert/generate my ePubs and then close it. After doing that, I connect the Nook and manually copy that author directory over to the Nook in 'my files/books/' (I think that's the right tree structure...if not, you'll find it) and voila, your done. I always do a power off and restart after this but don't know if it's necessary for the Nook to rescan the SD Card.
Let me know if you know a way to specify the directory to place the docs in Calibre because maybe, just maybe I don't know how to use Calibre well enough.