When I first tried using the Nook for PC software it took me a while to figure out how to get my personal files into my Nook software. Here are the simple steps to get it done.
1)Open the Nook software.
2) Click "My Library"
3) Click "My Stuff". If you can't see the "My Stuff" link, expand the nook window. It seems to default to a size that hides this option.
4) Up at the top click the "Add New Item" button
5) Browse for the file and click the "Open" button. It will then be available in your reader.