There is only one solution to managing your ebooks that I have found that works for just about any reading platform and that is Calibre.
Calibre is an ebook management program that allows your to create your own ebooks from a document, html and convert between most formats to allow you to put your book you your reader of choice.
Calibre can be downloaded from http://calibre-ebook.com.
There are versions available for Windows, MAC and Linux and they are updated weekly with new features and bug fixes as well as support for new readers coming onto the market.
It works well with all of the Kobo, Kindle and Nook eBook readers and hundreds of others. As well as support for programs installed on IOS and Android Devices.
One of the other great features is that it can download news feeds from many news sites and convert them to eBooks for later reading.
It can also function as a personal webserver for your books allowing you to download them to your device from a web browser. This works very well with both Android and IOS devices.