Say what you mean. It’s so simple in books, right? If it’s an important idea, bold it. Or maybe italicize it. If it’s a section header, make it big. Chapter title, make it really big. That’s all there is to it, right? Not quite. Not anymore.
The standard manuscript format doesn’t really apply here. It’s not a bad starting point, of course; most book designers are used to starting with manuscripts that conform at least visually to some form of a standard manuscript format. But there’s more to be done before the manuscript is ready for book design.