I start out in Scrivener and end up in HTML. Scrivener is great for the actual writing process, although it takes a bit of learning to get used to.

I wrote up on my blog about creating the various versions http://rachelandrew.co.uk/archives/2014/01/07/html-epub-mobi...

I've also recently presented on how to build books in CSS and HTML and the slides and various useful resources are here: http://rachelandrew.co.uk/presentations/css-books