It's almost a "hidden feature" currently, but near the top of the Markua manual we say:
"Markua is a plain text format. Markua is basically Markdown, minus all inline HTML except comments, plus a number of extensions to support everything you need to write a book or create a course."
So, this means you can do comments in your manuscript that won't appear in your book, like this:
%% This comment in the manuscript will not appear in the book
You can also do this:
<!--This comment in the manuscript also will not appear in the book-->
So, if you type this in your manuscript:
This is what you will see in your book: