How do you determine the ToC in a PDF?

I noticed unchecking PDF Outline will remove it entirely, but is there a way to specify only Chapters (and not scene headings) show in the outline?

( By outline I am talking the left pane in OS X Preview which typically has the Table of Contents and lets you click on chapter names like a bookmark).

The PDF outline lists any item that generates a visible title. For more control, you would probably need to use a PDF editor.