The first stage in getting what you want is to make sure the section types are assigned to the correct folders/documents in your binder. This can be done automatically by hierarchy of your binder, or manually if you don’t have a consistent organization to your parts, chapters, and scenes.
So, open your draft (aka: “manuscript”) folder in the outline view, add in the “section type” column.
Verify that your part folders/documents are all assigned a section type that is different from the rest of your folders and documents in the draft folder. Likewise, all of your chapters should have a section type that’s different from your parts. Finally, if you broke your chapters down into scene documents, then make sure they have a different section type from either your parts or your chapter folders.
You can do all that automatically by going to Project->Project Settings->Section Types, and creating or verifying that there are Part, Chapter, and Section or Scene section types. Then going to the Default Types by Structure tab of that same window and assigning the appropriate default section types to the correct outline/binder level. I recommend this if you organized your parts, chapters and sections in a way that this interface can distinguish, as it will save you a lot of manual assignments. If you have a few oddball documents that don’t fit this hierarchy, then they can be manually set.
So, that’s a lot of words for something that I can do in a few clicks…
Next steps will depend on what your final format is supposed to be for. Self-publishing? Submitting to agents/editors/writing group (aka: double-spaced, 1" margins…)?
For the later, there is the “Manuscript (Times)” format, available for PDF, Print, and most word processing output formats. That should be your starting point if you’re NOT self-publishing, because it gets you 95% of the way there.
If you are self-publishing, there are going to be more tweaks, I believe, but I’d still start with one of the Paperback presets.
Then start playing with the various section layouts, assigning different ones to your parts, chapters, and scene section types, compiling and then changing which built-in section layouts you use for each until you’re close to what you want it to look like.
Finally, once you’ve found something that’s close, CTRL-click on the format you’ve been using, and “Duplicate & Edit Format” to continue your customization. Note that <$R> (upper case!) is the basic roman numeral placeholder tag, but I’d go ahead and customize it to be <$R:chapter> when you’re customizing your chapter titles, as that will make those roman numerals distinct from any other <$R> placeholders in use.
Hope that was helpful.