Welcome to MobileRead, Angelstark! Unfortunately, I don't think that anybody has discovered a way to get covers for PDF's. Same for books with DRM that came from other sources like Sony or Kobo. I've read on another forum that BN is looking to fix this problem on a future update. You can make the covers show for non-DRM EPUB files, although sometimes it requires a calibre conversion. There is a long thread here with several tips on how to do that.
https://www.mobileread.com/forums/sho...d.php?t=107318
In regards to your second question, I do not think it is possible to turn your PDF into the same formatting that a NOOKMagazine does. That would be cool though!