You need to create a custom CSS and direct ID to use it in the export settings. And then you need to map all of your paragraph styles in every chapter to styles in that CSS. This is easy to fix if you create a template to house all of your paragraph and character styles because you can then sync all of your chapters automatically to the styles in your template.
1. In the template's Paragraph Styles panel, selecte Edit All Export Tags from the panel menu. For each style, map it to the appropriate CSS style and class that you set up in your custom CSS file.
2. From the book panel, select all chapter files and sync them to the template's paragraph styles using the icon in the book panel's toolbar.
3. From the book panel's menu, select Export Book to EPUB and designate that the custom CSS file be used. (Note that ID uses that file but renames it to template.css during export.)
I can't empathize enough how important it is that you remove all overrides in your files to keep your CSS clean.
I found a helpful discussion of some of these issues at http://www.creativeprogression.com/taking-the-cs5-5-epub-plunge-export-tagging-to-the-resc ue/