I use Calibre to manage my epub files. They would be a mess without it!
I would like to set up a second library just for my Kindle freebies, but I haven't figured out how to get them from Amazon onto my PC. I'm thinking it's from lack of effort. I had a Kindle reader on my last PC but I couldn't locate the books that I downloaded into it. I think it wasn't the right software, but I haven't looked into it since getting my new computer.