The eBook manager calibre is good for managing files too (donateware.) You need a PC. Download your eBook then use calibre's Add Book icon. calibre can also convert to/from many formats. When you plug in the USB cable calibre discovers the nook(Color) and allows you to push the book down. The books show up on the main shelf. Back in calibre you can see what's on the nook and remove the file when you are done.
calibre also allows you to edit the metadata about the book to control the title, cover, etc. Good for dealing with "raw" data like text files and HTML pages.
I had to load Adobe's Digitial Editions to manage protected files that I download from out library. It can manage downloaded non-protected files as well.
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