There is a tutorial over at lynda.com on the subject entitled InDesign CS5.5 to EPUB, Kindle, and iPad. It's by Anne-Marie Concepcion of InDesign Secrets.
I think it's worth becoming a member to watch it if you aren't a member already.
Also get InDesign 5.5 if you don't already have it. They keep making major improvements to the epub export process and 5.5 is by far the best yet.
If you have InDesign 5.5, you can pretty much design the document for print and then use a few features (like the new articles panel) to optimize your document for epub. This is less true if you are using InDesign 5 and it's even worse if you are using versions 3 or 4.
On output, InDesign turns all your paragraph styles to p tags with the class name being the style name. Character styles are span classes. You can use DreamWeaver to edit the css and html output if necessary. You do that by unzipping the epub file. I created a site in Dreamweaver that I call epub so I can do global search/replaces to my epub files if need be.
Some of the css styles, InDesign generates do not work in most epub readers so you may need to edit the css. Just check your output on as many devices as you can and learn what works.
There's a really great guy on her named pdurrant who has created a ton of applescripts including ones that zip and unzip epub files, run epubcheck, and create mobi files (for kindle). I've incorporated a bunch of them into my workflow.