Hi! The good charleski is probably helping you, but I'll give you a general tip: The epub output of Indesign is seriously flawed, and their advice on how to generate epubs with the book structure is ridiculous. I'd recommend you to merge them into a single document, apply styles and export epub. Then use Calibre to convert it epub -> epub with structure detection for page breaks and headers. The style names are kept as html class tags when it's exported to epub. Calibre is also perfect for adding metadata such as covers.
Also note that Indesign "encrypts" the fonts used, no matter what their Copyright status is. This makes the fonts unusable in many readers. We workaround this by opening the finished epub file with winrar, removing META-INF/encryption.xml, and replacing the font files embedded in the epub.
I work at a publishing house, we have developed a set of detailed instructions + a template file for making epubs from Indesign sources. PM me if you're interested in a google-translation from Norwegian, although some of the instructions are specific to how we do things.
Last edited by Man Eating Duck; 08-13-2010 at 01:42 AM.