What is the difference between Chapters and Scenes, and how do they integrate with one another?
The content of your story can indeed be contained in both Chapters and in Scenes. Chapters can contain one or more Scenes, while Scenes can “belong” to one and only one Chapter. In addition, Chapters may also contain no Scenes at all.
For example, in the Chapter “Mr. Brown and Mr. Black have lunch”, you may have several scenes, such as “Mr. Brown goes grocery shopping,” “Mr. Black picks up sausages at the deli” and “Mr. Brown burns the toast.”
Scenes can be added to Chapters simply by dragging a Scene into a Chapter in the source list, or by setting the Scene's Chapter in the metadata pane.
When you look at the top of the Chapter Editor window, you will see the “mode bar” which allows you to display text from the Chapter you are currently viewing (Show Text from: Chapters), text from the Scenes contained within that Chapter (Show Text from: Scenes), or text both from the Chapter and the Scenes contained within it (Show Text from: Chapter+Scenes).
When you are displaying text from Scenes only, the Scenes will be displayed in the order they appear in the source list (the sidebar- like display of views on the left of the window - with every other scene drawing on a subtle background to differentiate one scene from another. When you are displaying text from Chapter+Scenes, the text from the Chapter text will appear in the white space at the top of the editor window, above the Scenes text.