I've been emailing my non-amazon books to my
me@kindle.com address, so that they show up in the 'cloud' tab of my 'docs' screen. That makes things pretty straightforward as far as keeping them in the cloud, as long as you don't have very many of them (at least with box or dropbox you can create a directory structure to organize your books if you have a lot). Also, it only works with non-drm files.