Even though this is an old thread, thought many (like me) may still be searching for an answer. I figured it out, at least for my problems. I used calibre to fix metadata, get cover pics, then convert other formats to epub for my Nook Color. But, the epubs I got from the Gutenberg site, libraries, etc. I didn't convert after doing that since they already were epubs. I just downloaded to my Nook. I posted a couple days ago for help, but then figured it out.
See my thread at:
Hope it helps!