Most of the built-in templates and presets will handle chapter numbering for you, as this most often busy work that computers do better than humans. But if you do want to type in your own titles, right into the text editor from start to finish including the number, that is fine we all have our preferences. But to work in this fashion you will need to disable some automation.
You might find this prior thread insightful. You’ll note one of my first suggestions is to try using the “Original” compile preset, which doesn’t add anything to your text at all (save for page breaks when a folder is encountered), does nothing to the formatting of the text and mainly stitches the Draft files together end to end into a single document.
I’m not sure what your Binder looks like so I can’t be very specific here, but it sounds like it would benefit you to scroll through the Contents list in the compiler and make sure everything that should be is checked off in the “Include” column.