Well, this is where the real problem lies - InDesign is a very powerful program for creating fixed layouts, but simply uses the wrong idiom for ebooks, which are fundamentally based on having a reflowable, flexible layout with relative positioning.
There are no 'good' settings for individual styles, since they all need to be edited after export to convert the measures into relative sizes. The important thing, then, is to use styles as consistently as possible and tag them with names that will make it easier to work out what the css selectors are referring to. One option is simply to decide on a standardised set of style/class names and create an external stylesheet, then link this into the ePub on export.
BTW,
here's a couple of pages on all the things you needed to do to an ePub exported from CS3 just to get it compliant. Luckily, things have improved a lot.