The nested cards are definitely a great tool to create the structure. Even after the initial outline, I came back to them every now and then to re-evaluate the logic flow or to place new sub-topics that came up.
The biggest win for me was how Scrivener supports an iterative workflow. I started with keywords on the cards for what a chapter should be about, wrote a few sentences describing the keywords inside the document, added context so the sentences became paragraphs, fleshed it out and polished it. During this process I used colour labels in the outline view[1] to keep track of the state of a chapter.
All this took away the pressure to write a long, good and coherent text. I only had to increment little by little to which my brain had far less resistance. If I was stuck on a chapter or couldn't motivate myself to keep working on it, I switched to another one and do a little work here, a little work there.
Also the usual Latex applied as well: I only focussed on the content and didn't format anything properly and left placeholders for images. I used Pages (the old version with two sided layout) for the final assembly where I only had to worry about layout and not on the content.
I also used it just for my thesis. Most helpful feature was being able to jot thoughts down into cards that could then be moved around and organized until coherent chapters coalesced. If you do the same in a plain outlining tool, you may find yourself distracted by the order it pre-imposes.
