1. Book is entirely written in LaTeX, every chapter in it's own file, master doc with everything combined. I really like having different gutters for left and right pages, ultimate control over formatting, fancy things like Lettrine, header layout and design etc. When I want to do something across the entire doc I write a new command and can use it anywhere.
I Create perfectly formatted print-ready pdf to go to printers directly from this.
2. Run LaTeX file through pandoc to create an ePub.
A little known trick that is now supported by pandoc is conditionals in the LaTeX doc, so when formatting gets hairy I declare commands like this in the master LaTeX document:
\iftoggle{ebook}{
\newcommand{\textbreak}{\newline\hrule\newline}
}{
\newcommand{\textbreak}{\begin{center}\LARGE{$\Psi\quad\Psi\quad\Psi$}\end{center}}
}
3. Un-pack the ePub and tune some of the html/css to my personal taste, then pack it back together. I run it through kindlegen to make sure it's valid, and I have an epub/mobi ready to upload to stores.
I like this workflow so much I'm using it again for my next book