My projects have all be organized as seen on the left, here:
But I watched a video in which the writer kept the front matter and back matter outside the manuscript, as seen on the right. That would have some advantages for me.
How do I set it up so that the front and back matter are compiled into the final document in the correct order?
You can select any non-Draft folder, or any one of its sub-items, from the “Add front matter” drop-down menu under the Contents list in the compile dialog. The items will then be added to the top of the list, coming before whatever you’d normally had set to compile. At that point they’ll be treated like the other items in your list as far as separators, formatting, etc.
The advantage to this is that you can easily swap out different sets of front matter, or exclude it altogether, for different types of compile formats. We’re looking to add a little more to this feature in the future, and to add a similar “Back Matter” feature as well. For now, back matter still needs to be included in your Draft.