I don't know if any of you have tried formatting your own ePub yet, but I'm in the midst of doing one now in Adobe InDesign CS5.5 and it's fairly straightforward. The entire document lives inside of a continuous set of threaded frames and the graphics are placed inline to the text instead of being placed externally.
The one problem that I've encountered is formatting footnote callouts.... they come out looking honking HUGE in the final ePub document.
Is there a way to apply a character style to footnote callouts in order to reduce their font size?
They footnote callouts are just hyperlinks that are internal to the document, so there may not be a way to style those yet in the XHTML setup for ePub format... but I can't find any documentation on how to style hyperlinks... not yet anyway