I've had projects where it's just one big .tex file including all the macros and content, and projects where there's a whole file hierarchy of chapter subdirectories and layers of \inputs and macro files and... It can sort of get out of hand for me, where it makes sense in the moment and then looking at it a week later it's a puzzling labyrinth of files.

I guess it depends on the nature of the project, but do you have a go-to way that works for you in most cases?