Adding Non-Fiction Book Parts

I have a non-fiction book that have three major parts. Think of the tree as:
Part I Title
Chapter 1 Title
Chapter 2 Title

Part II: Title
Chapter 6 Title
Chapter 7 Title

Part III: Title
Chapter 11 Title
Chapter 12 Title

In order for me to create the chapters, i follow the instructions to create Folders under the Manuscript main folder. How would I add the part Folders? Or do I add pages between chapter folders?

You can select a set of your existing chapter folders and use the Documents->Group menu to create a “Part” folder for that selection; that’s the easiest way to make your binder structure conform to your structure. For parts that don’t exist, create the part folders first, and put chapter folders inside them.

However, It’s my understanding that the non-fiction template (I’m assuming you created your project from one of those templates…) and the compile presets are more of a technical/academic bent, so that you have hierarchical numbering rather than “Part 1” and “Chapter 3” style headings. Others may be able to help you sort out the compile settings to conform to how you want the output to look. If you just want the formatting to look like a novel, using “Part III” and “Chapter 9” as headers, then you can probably go with the “Novel with Parts” presets as a starting point.