I’m trying to compile my project into a PDF, and want to make it so the chapters have the titles I gave them and aren’t just numbered. The issue is only the first and last chapters have their proper titles, while none of the rest do. The difference is those two are single documents, while the rest are folders with a document for each scene. What do I actually have to do to fix this, and why was compiling made so complicated in the first place?
Because it allows it to do a bunch of useful things.
The flexibility it offers couldn’t otherwise be.
But it is actually not complicated, at all. Complex? yes. Complicated? no.
It seems that at this point you have pretty much everything to learn about it (no offense intended) so I am not gonna go into the specifics, but will rather point you in the right direction as to where to look.
→ Note that the following are screenshots taken from the Windows version of the software. They look different, but they should match.
In your project, to the right is the inspector.
Have it display the metadata panel. 
In this part of the panel :
… have your documents that don’t compile the way you want them to, be assigned, using the dropdown menu, to the same section type as your documents that compile properly.
You are most probably currently set to compile according to binder’s structure.
In which case what I just suggested is not really the ideal solution (somewhat more of a hijack, depending on how one would look at it), but still I believe it’ll get you where you want to be for the time being.
(For the folders you mentioned that contains scenes, only change the assignation of the folder/parent document. Leave the scenes inside them as they are.)
. . . . . .
Alternatively, if indeed your documents are assigned to :
the proper way to do things would be more like to go to Project / Project Settings..., and fix the section type assignation here :
. . . . . .
And now for the advice no one ever wants to hear: you should read the sections of the manual pertaining to the compile process, at least once (with a test project open, reading slowly, trying everything depicted), as otherwise most things will indeed be (and remain for a long while) complicated.
Hope this helps.
Any patronizing “tone” unintended.
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Before trying to read the manual, I recommend spending 25 minutes watching Literature & Latte’s official videos on Compile — only parts 1, 2, and 4 unless you want to learn structure-based Compile (which I do not recommend).
Here’s my workflow for Compile: