Hello,
I’m a new Scrivener user and I’m trying to set up a project for my PhD draft. I couldn’t find a dedicated PhD thesis template, so I settled on the ‘General Non-Fiction’ one, which seems to be adequate. After spending quite some time going through the tutorial and watching the different videos, I’ve set up a basic filing structure for my chapters and have tried to allocate Section Types to all my various files as per the tutorial. I did this using the ‘Defining Default Section Types by Structure’ advice. There seems to be a problem, however, In this template, the ‘Draft’ is renamed ‘Manuscript’. The Manuscript comes up as a Root Folder, along with Front Matter, Back Matter, etc. I’ve set these Root folders to be called ‘Parts’. However, the Manuscript itself refuses to be labelled ‘Part’ and comes up as a ‘chapter’, which is the section type for level 1 folders. If I override this manually, and change the Manuscript folder to ‘Part’, it automatically changes the level one folder beneath it to a ‘Part’ as well, when all the level one folders should be labelled chapters. If I change the level one folder back to ‘Chapter’, or simply select the structure-based option from the drop-down menu in the Inspector, this changes the root Manuscript folder by default back to chapter too. This is REALLY annoying. Why won’t it just label it the way it says it is going to when I set up the structure in project settings? Is this a bug?
No, it’s not a bug. “Root Folder” in the context of “Default Types by Structure” means top level folder within the Draft/Manuscript folder. The draft folder is special and cannot have a section type assigned.
Further, the front matter and back matter folders are intentionally separate from the main manuscript and do not follow the project default types by structure. This is so that their pages can be unnumbered, or follow completely different numbering schemes, vastly different formats, etc… They’re intended for a published book on a shelf, or an ebook—where title pages, copyright pages, dedications, ads for more of the author’s books, and so forth go. These folders are very useful for me, a fiction writer, as I can customize them for various distribution channels quite separately from the main manuscript. While I’m certain that academic writers use them, I’m equally sure they are not often used as manuscript parts with chapters in. 
To summarize: All your manuscript parts should be inside the Manuscript folder, which does not itself have a section type. You should consider the Front Matter and Back Matter folders for things that really aren’t part of the manuscript itself but which might change with your audience. With any luck, real academic writers will chime in here with examples of proper usage.
Thanks so much!
When I go in to the ‘Default Types by Structure’ settings and select ‘Root Folders’ though, it highlights the Manuscript, Back/Front Matter, Research etc. by default. Are you saying that these shouldn’t be ‘Root Folders’? If so, I’m wondering why they are selected by default as this.
The default setting for these root files (Manuscript, Notes, Back/Front Matter, Research etc.) is n/a. Is that the setting you leave yours on?
Do you assign the folders/documents within Front and Back Matter a section type also, according to the ‘Default Types by Structure’ tool?
Thank you!
You’re right, and I’m wrong; I usually don’t think of these things in language, but as diagrams inside my brain. Let me see if I can back up and explain it correctly.
First, yes, the default by structure for root-level folders is N/A. That means that despite the fact that you can set different section types in the Default Types by Structure, these folders are not considered a “real” part of the final product–only their contents are. I personally choose to change this–my Draft folder has been given the type “series” because that’s what it is 
—but it doesn’t much affect what happens in compile. Basically, it gives me an alternate way to access my series title if I rename the Draft folder to to my series title, but otherwise it doesn’t mean a lot. I’ve never tried compiling a box set—I may yet have to include another level of folder and call it “series” instead to get the result I want.
The Front Matter and Back Matter folders (hereinafter “F&B”) aren’t intended to be included wholesale, either. Rather, their subfolders are intended to be included in appropriate output formats. For example, you’d include only the Manuscript subfolder as front matter for submission to an agent, publisher or editor (thesis committee? ), only the Paperback subfolder as front matter for creating a PDF to upload to Kindle, and so forth. If you require front or back pages to have different headers and footers from the main body of your work, the F&B folders are the way to achieve this.
Whatever documents you do include from the F&B folders are treated as if they were stuffed inside the Draft folder at the front or the back, respectively. Personally, I have several custom section types for documents inside the F&B folders, and none of them use Default Type by Structure.
To summarise, the Draft folder is the container for all matter to be compiled. That is its primary function and it is treated differently from all other folders. Front and Back Matter folders exist to contain book cover images, allow for different front and back header formats, as well as accommodate differing front and back requirements in various publication formats. If F&B are compiled, they (or their selected sub-folders) will be treated as if they are contained within the Draft folder.
I hope that’s clearer.