I have yet to buy any ebooks from amazon, just downloaded most of mine through "3rd parties", and the kindle is a wonderful device for that, thus I can share my books with whoever I like.
Or setup a spideroak sync folder for the ebook-folder on your android, and just sync your non-amazon books through spideroak.
It never works on my mobile for some reason.
It's not perfect, but it's very good and much nicer than doing it manually. Especially for managing collections. Regularly updated too.