Ereaders like the Kindle are designed for fairly basic text viewing and reflowing. Think more in terms of a novel rather than an elaborately formatted reference book. Nevertheless, you can use cascading stylesheets (CSS) to create most styles you could ever want. CSS allows you to expand the formatting capabilities of HTML almost as far as you could dare. However, you are reading on a small 6" or 7" screen so things like outlines with 9 sublevels will look like poop, as do multi-column tables. Subtle formatting changes might go unnoticed. You basically have to divorce your mind from a 8.5" x 11" printed page format to achieve something that works and looks good on a small screen.

I'm not sure at all what kind of formatting you desire that you cannot achieve with HTML, except for font substitutions of course. If you could post a screen shot of what you are trying to achieve perhaps we can better assist you.