If you're going to do your own typesetting and everything, markdown won't be powerful enough for what you want. LaTeX can do all this for you, or you can use so

If you're going to do your own typesetting and everything, markdown won't be powerful enough for what you want. LaTeX can do all this for you, or you can use something like Scrivener which is much more of a WYSIWYG tool. I've used markdown for shorter works, and even for them markdown quickly becomes annoying and too simple for my use (especially since many platforms and even the CMS for sites I do paid engagements for don't support vanilla markdown). For longer, printed work with an outside publisher and editors, surprisingly enough Google Docs works really well (I'm using it for 15+ page published PDFs, and authors I know that have written technical books you've probably heard of swear by it), but it will be a pain if you're doing all the formatting and typesetting as well.