Compile is Scrivener's term for exporting output. How your project appears when you're writing in Scrivener is not necessarily how it will look when you print or make it into a Word document--the output
Compile is incredibly powerful and customizable and that makes it complicated.
Expect to spend a couple of hours of trial and error to get Compile to be satisfactory for your project. Don't wait until the last minute before a deadline to tackle Compile settings. Instead, work on your Compile settings, bit by bit, over time. Also, most likely Compile will not perfectly format your academic manuscript. Be prepared to do some formating in Word as a final step.
These two tips for Compile may not solve all your problems but can help:

A basic overview of compile : Scrivener's Quick Start to Compiling (6 minutes)
Compile uses Scrivener's section types.
Confusingly, Scrivener uses the term "section" to mean something different than its use in Word.
In Scrivener, each piece of your project---a part, chapter, document--is a different section type. Each piece should be designated as a "section type" in your project, depending on how you want the piece to be Compiled.
Not specific to academic writing but nonetheless clear & useful: How Scrivener's section types relate to compile
Not specific to academic writing but also helpful: step by step layout & compiling tips
"Manuscript (TImes)" is the recommended compile format.
To make changes to this format, you'll need to make your own format. Select "Manuscript (Times)" and "duplicate and edit format." Give the format a name that makes sense to you--"My Times New Roman format" or "My thesis," for example.

Notice there is no "save" for Compile settings.
Confusingly, if you close or leave "Compile," any adjustments you made will not be saved.
To save Compile settings, before you close or leave "Compile," click "compile" as if you were going to print or export the project, then choose "cancel" on the following screen.
Automatically include your name and title for the header:

Page number settings;

The <$p> is a placeholder for sequential page numbers.
If # appears between your documents... that is the default Scrivener separator and you can remove it:
Scrivener--> settings --> general:
