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InDesign produces tags with complete reliability. I think it is best to use those and create a new stylesheet (or stylesheets) for ebooks. Certainly for e-ink Kindle books this is the least painful way to go, seeing as Kindle decides which fonts are used anyway!
Since my earlier post I've decided to use Indesign's export tagging to assign h1, h2, h3, etc and p tags to every paragraph used. I also assign a class e.g. myh1, myh2, plus various different paragraph styles based around what sort of spacing and other styling each paragraph style requires.
I have also created several stylesheets, and used CS6's Additional Stylesheet feature to include these. This enables me to keep several sets of styles, and decide whether or not to override what InDesign exports (if it isn't working - as seems to usually be the case).
You can even have different stylesheets for different e-readers, all contained in the same epub. It isn't quite the nice tidy solution I expect from InDesign but it does work if you know what you are doing with css, and also means you can keep editing in Indesign and re-exporting epubs without having to then re-edit the Indesign-produced stylesheet to put the margins back in every time you do a new export.
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