There are a couple places to look:
This SO post explains some of the internals of the epub format: Reading ePub format. Some of the information is specific to Objective-C (so it won't be usable to you), but at least you can get a sense of what the epub format looks like.
Depending on where you're getting the .epub files from, you'll either need to download them or use the cordova-plugin-file to read them from the local device. The cordova-plugin-file has really poor documentation, but there are a few other resources out there if you need more help:
Raymond Camden has a few examples on his blog like this one: http://www.raymondcamden.com/2014/07/01/Cordova-Sample-Check-for-a-file-and-download-if-it-isnt-there. It's worth looking at what he's done.
For what it's worth, I also put up some code on SO to show how to browse through the device and collect the available files: How to get documents in an android directory that PhoneGap will see.
