For us to help you more, you need to tell us what version of InDesign you're using. InDesign has made significant improvements in EPUB export with every version from InDesign CS 5.5 onward to the current InDesign CC 2014.
The best source of information on preparing files in InDesign are the videos by Anne-Marie Concepcion on Lynda.com. She has videos from CS5 onward. You can get a free week's subscription to Lynda.com.
The best book on eBook typography I have seen is called eBook Typography, by Chris Jennings on the Apple Store.