Formatting a Novel with Parts

I’m writing a novel with parts, but I didn’t realize I had parts until I’d begun drafting, so I didn’t use the “Novel with Parts” template. So my structure is Manuscript --> Part (folder) --> Chapter (folder) --> scene(s) (text docs). However, Scrivener sees all my folders as chapters even though they’re nested, so I end up with Part 1 labeled as Chapter 1 and Chapter 1 labeled as Chapter 2.

How do I make scrivener see the higher level folders as parts?

When Compiling, just select the formatting presets that end with “(with Parts)” from the Format As list. That should be all you need to do if I understand correctly.
All the best,