Step Three: Format and compile your body material
Scrivener is going to format our body text’s headers, titles, and footers automatically, but it’s up to you to complete the formatting of the text itself. This means review such things as your italicizing and bolding, line centering, first line and hanging indents, etc.
The reason this is left up to you is that the compilation process allows you to automatically format ALL text, but I’ve found this process to be a bit too strong. It seems to preserve font-specific formatting like italics, but it steamrollers such things as line centering.
For body text this layout uses 11-point Adobe Caslon Pro throughout.
Here’s the first page of my body text, shown as-is in Scrivener:

Start by selecting the entire body beginning at the very first chapter:

Hit “File / Compile.” Under “Contents” set it up so that part title and deliberately blank pages are included “As-Is,” but that all other pages are subject to the compilation formatting steps I’m about to describe.

For Separators, choose “Page break:

Now we come to formatting. It’ll take several steps to properly format the body pages, but this is where you can really start playing around with the look and feel of your book.
Here are a few sample post-compilation body pages so you’ll know what we’re shooting for as we go through this process.
First page (right-hand / recto):

Second page, left-hand / verso of first page (note the page number is 2, which is exactly what we want):

And third page, right-hand / recto:

(With respect to the recto running header: it’s also a common convention to insert the chapter title where I’ve inserted the author name. Shortly I’ll show you how to customize your header and footer titles.)
So: choose “formatting.”
First, ensure that the “Override text and notes formatting” box is NOT checked. This will preserve any in-text formatting you’ve done, like line centering. (But obviously it’ll preserve any formatting inconsistencies/errors, as well, so a careful review is merited.)
If you’re using an Epilogue like I am, select the Level 1+ folder.

Set the page padding to 8 lines.
Under “Options” make these selections:

Under “Level Settings” make these entries for Title Prefix and Suffix,

And this entry for Text.

Select the body text and use the formatting toolbar to ensure that it’s fully justified so you don’t get a “rag right” appearance.

Now jump down to Level One headings.

Again, ensure the “Override text and notes formatting” box is not checked. Set the page padding to 12 lines. Under “options” set the following:

Under “Level Settings” do this for Title Prefix and Suffix,

This for Title Appearance,

And this for Text.

When you’ve made all those selections, hit “OK.”
Select the title and use the formatting toolbar to center-justify it.

Also select the body text and full-justify it like we did in the example above.
Now switch from Formatting to Page Settings. This is where we’ll set up headers and footers.

Several things to take note of:
- The page margins I’ve set here are CreateSpace’s minimum requirements for the 6X9 size.
- The Header and Footer setting showing in this pane is the default for right-hand / recto pages. Go ahead and set yours this way, and ensure that you’ve checked the “No header on first page and pages following page breaks” and “No header or footer on single pages” boxes.
- The header font and footer font are one point diminished from the size we used for body text, but the same font we use for titles throughout the book.
- See under the header where I’ve included the placeholder tag <$author>? That’s what tells Scrivener to include my name in the recto running header. There’s a complete list of available placeholder tags on Scrivener’s Help menu under ”Placeholder Tags List.” Check out “<$sectiontitle>” if you’d like to insert chapter titles rather than your name.
Now choose “First Pages” and check to see that this is how things are set up:

And fill “Facing Pages” in like this:

Believe it or not, we’re finished with the body. Hit “Compile” and for convenience’s sake save your second PDF to the same directory where you saved your first one, as something like “TITLE-body.pdf” so it’ll be easy to recognize later.
Once you’ve compiled your body text I suggest you inspect it in your PDF viewer. This is a good time to make corrections and/or tweaks.
Something you may notice as you inspect your body PDF is that chapters subsequent to Chapter One may begin on left-hand / verso pages. Conventionally that’s OK; they can fall either recto or verso. But if you’d like to force a chapter that currently begins verso to begin recto, it’s simple to do so by inserting a deliberately blank page immediately prior to it. Beware, though, that this repagination will cascade through the rest of your document, and you’ll need to verify the location of each chapter heading throughout for its own recto / verso location.
A sidenote on footnotes / endnotes: I haven’t addressed this issue because I don’t have any in Gunrunner Moon. They’re not difficult to set up in Scrivener, though. Experiment with the “Footnotes / Comments” pane in the Compile wizard to get the look you want.