I'd suggest Calibre for the digital books. I've got somewhere around 2K books, and there's no way I could keep track of all of them without it. It lets you edit metadata, convert formats, manage sideloading, track series, track what you have and haven't read, and a million other things I probably haven't even thought about doing with it yet. It's pretty spectacular.
There's a forum for it here on the site that should be able to answer any questions you have about it.