Get up and running with Scrivener. The videos below supplement Scrivener's interactive tutorial (available from the "Help" menu in macOS and Windows and from the projects list on iOS). Also available on YouTube.
Figure out the structure of your manuscript in Scrivener's Draft folder.
Using Scrivener's corkboard to work with a bird's-eye view of your writing.
How to use Scrivener's powerful outliner to plan or rework your manuscript.
Using synopses to plan your writing or to get an overview what you've already written.
Get messy with Scrivener's freeform corkboard mode.
Using Scrivener's "Arrange by Label" Corkboard mode to track threads such as storylines in your project.