I have chapters within sections. For example, section 1 is Cars and has related chapters under it. Section 2 is something else with related chapters. I have this with each section is a folder at the root level, under manuscript, while each chapter is a sub-folder under the section.
When I compile it, each section is getting assigned a chapter number. How do I avoid this?
Everything is explained in Ed Ditto’s book
“How to Format Your Novel for Kindle, Nook, the iBookstore, Smashwords, and CreateSpace…in One Afternoon”
This book is for Mac users. Plus, why should you have to buy a book to learn something that should be set out in a manual?
There are differences between the Mac and Windows version, but sometimes getting suggestions from someone else can give new revelations. But you’re right. Read the manual. Chapter 23.8 in the Windows manual.
I long for the day when version 3 comes out, and we poor Windows users get parity. 
From what has been said, there’s still going to be a lag between Mac and Windows – just not years, but now months.