Those are great ebooks, but I think you'd find more of your questions answered in the series of video tutorials, "InDesign to EPUB, Kindle, and the IPad" that I did for Lynda.com this spring:
http://www.lynda.com/tutorial/75445 (that's the CS5 version, I also did a CS4 version ... you can find it on the site).
The videos have a ton of info on fixing styling and local formatting for EPUBs in InDesign, manually or with free scripts, and also how to manage the layout flow for complex docs.
There are few free sample videos you can watch but to see them all you need to get a sub to Lynda.com... it's just $25/mo and you can cancel anytime though.
But I have to tell you, especially for complex docs, you'll find InDesign CS5.5 MUCH easier to use to make EPUBs. If you can possibly upgrade, do so. In CS5.5 you still have the same layout options as in earlier versions, but you also have the option of dragging and dropping frames to an Articles panel, and then rearranging them in the Articles panel to force an export order. (I'll be doing a CS5.5 version of the EPUB title in a few weeks).
Anne-Marie
co-host, InDesignSecrets.com
twitter: @amarie