InDesign has a full set of epub:type semantics built in. They are an added layer of semantic inflection that can be applied at the object level to provide an outline to the “bones” of content. Wherever possible, let the HTML do the semantic heavy lifting for you. In a simple chapter, have the body of that chapter wrapped in a section tag. But, in order to distinguish one section from another, you might consider adding in some code that communicates a little more information.