From my short experience, let me summarize some things you must take into account when writing a book. Its is not a mechanical process, it is more related with inspiration, but we must be constant and productive.
It is a fact, a law of universe. You could desire write but some days your brain is not clear enough, agile enough, fresh enough to write as you like.
Don't force yourself. Don't hate yourself to be unable to write as you would like. Relax. Disconnect. Put your head in another tasks. Do some sport.
The best thing to do when today isn't the best day to write is not to write.
Yes, markdown syntax is great. It is simple, clear and powerful.
At the beginning, if you come from a complex word processor like Word, Pages, LibreOffice or similar, you feel nude, but later you will appreciate that nudity.
Markdown separates your raw writes from the final visualisation.
People tend to drown looking for the perfect tool to make the work. My advice is don't bother you, a simple text editor is enough to write any kind of book (otherwise ask to the hundreds of people that have written using a typewriter). Personally, I prefer a simple text editor over a word processor, because the first isolates the content from the way to visualise it.
Of course technology can improve the way we work. We have tons of text editor, classics like vim or emacs text editors, the new ones like SublimeText, TextMate or the Ulysses application, and also, many online text editors, like dillinger.io or StackEdit.
Some kind of books, like technical books, are plenty of cross references pointing to other sections, chapters or samples. It is vital for the author to maintain these references updated and organized.
When using markdown a tend to organize the book as follows:
chapterNumber_chapterName.md
1- Introduction {#ch1-introduction}
1.1- Some section {#sc1-some-section}
These simple tips help you organize the whole book references and simplifying the process to create cross references.