After playing around a little bit, I figured out that the most comfortable way of writing a story is to put everything in scripts. (Don't ask, I like the bit more control over spacing that it gives you.)
One big advantage is that it leaves the main body of pages free for notes and those notes can be seen in the preview from the editor main screen, which is massively helpful.
The only downside that I can see is that it throws the automated word-count off the mark pretty badly?
Is this an issue for other parts of the site? Any fix? Should I just copy some text into the main page body as surrogate when everything is done.