I read about people having problems with formats on Smashwords and I just scratch my head in wonderment. I don't think I'm doing anything other than following the style guide and building my document in OpenOffice and saving to word doc. I've never encountered any problems, either I am lucky or better at formatting my document than I think.
I don't do anything really that different, I just dump out the styles and don't get too precious about the formatting of the document because I accept it will be seen on various size screens.
Arigato,
Nick Davis