I've been using a workflow to generate epub + PDF for several books so far, and in my experience, using Markdown base files is very good: you can include images, links, etc., and then you can use pandoc (http://johnmacfarlane.net/pandoc/) to generate both epub and context source, also you can customize the templates used by pandoc to generate the context source; that way you can handle the pdf layout; however, you must remember that epub can't handle mathml; you must include equations as images, if you have them, and you won't have any real presentational features: epub is as simple as it can be. Like HTML in the early 90s. But this way works for me.