Formatting Chapters within Sections

I’ve trying to figure out the “right way” to set up the folders and files for my non-fiction book. The book is done and I need to get it into the right format.
In general, the book is set up like
[front matter]
Section 1
Chapter 1
Chapter 2
Chapter 3
Section 2
Chapter 4
Chapter 5
Chapter 6
[back matter]

To make this work, do I create a folder labeled “Section 1” and then subfolders for the chapter names and finally text files for the content of each chapter? If not, what do I do? This is what I’ve tried, however, when I compile it, my sections include the chapter numbers.