I always use ePub myself, but quite often I need to fix books up in Book Designer, which makes the best book file of any format that I have found, (and understand how to use). If I have an epub that I need to fix up, or want to embed fonts in etc, I like to run the file through BD for formatting. First I will convert the epub (via Calibre) to FB2. For some reason (that wiser minds than mine understand), I can't load Calibre created lit. files into Book Designer. FB2 loads nicely into Book Designer. The FB2 format seems to be alright for maintaining formatting and identifying titles and chapter headings. After I make all my fixes, I create an LRF. I usually then convert the new LRF back into ePub.
Many a man has dated a new era in his life from the reading of a book.
Henry David Thoreau (1817 - 1862)