Scrivener is built around a model where composing (the act of creating text, sections, outlining, etc.) is separate from formatting a final product where the all the indiviudual piece of your novel get threaded together into a final manuscript, word, doc, ebook, etc. Once you’re comfortable that model, compiling a manuscript for me it’s a three step process:
1- Assign the correct section types to all the parts of the manuscript. Scrivener does a pretty good job of this automatically, but I like to check in the outliner that every part has the right section type. Note: Folders have section types, too! These can be where titles and headers come from.
2- Once section types are right, I go into the compiler and assign section layouts for each type, such as part, chapter, body text for the output type I want like PDF, Word Document, Epub, etc. This is very important, this is where you tell the compiler when it sees section type “chapter” it should use a sepecific layout. Sometimes layouts aren’t what I want, so I have to go into the layout editor and modify them to my liking. This can be confusing and frustrating, so going in cold is a bad idea. Fortunate L&L has some nice videos that walk you the the processes.
3-Set the various book level parameters for the output in the compiler pane. There are a handful of them, but most of them should be obvious like the metadata for the book.
From my perspective, people often get hung up on step two because we often use the same name for section types (the tag on a manuscript component that tells us what kind of componet it is) and section layouts (the instructions for the compiler on how to lay out a section.) These are really very distinct things and it’s important to relate the right section type to the right layout or the compiler will not produce the result you want. Most people I know don’t find the section layout designer all that intuitive–YMMV.
Fortunately, there are lot of video tutorials, though sometimes you need to look in the Mac section. It’s worth going through those videos before tackling the compiler for the first time.
It is my sincere recommendation that you don’t tackle the compiler without first availing yourself of these videos–it will save hours of confusion and frustration later.
It sounds worse than it actually is–once you get the hang of Scrivener’s way of doing things, I find I can’t live without it. (I tend to write non-linearly, so it makes managing the jumble of chapters and scenes much more manageable for me.)
As mentioned by @kewms, its the power of making my research, writing, and editing jobs easier is where Scrivener really shines. The compiler is just the end stage that threads all the work together into a final manuscript or book.