Eiron, you have some good ideas there. The way I use Scrivener is actually a bit different than the hints I provided above. They could be considered the most “simple” interpretation of Scrivener’s features.
I suppose because of old habits dying hard, or just preference, I’ve always been one to prefer most of my notes to be embedded right into the narrative, which is where inline annotations shine. In the past, my precise usage of them has mutated according to whatever software I was using. Ulysses (not counting the latest beta) had a constraint where comments could only be in their own paragraph. It also had a single-colour highlighter. So I would use that highlighter to provide context for notes which had to, by necessity, be located away from their context.
Scrivener brings two new abilities to comments. Of course, being able to place them anywhere I like, and secondly, the ability to create links to other documents. So my usage has been mutating yet again, and I have yet to finalise where it will end up. If I do end up doing Nano, that will be the first big project that I use Scrivener for, and no doubt I will have a more concrete idea of how the application and I get along.
After a lot of thought, I decided to abandon my current usage of labels to define types of documents. With Scrivener, that is largely obsolete usage. I can simply create a Group called “Characters,” and fill it up with documents about characters. Ulysses has no such grouping available to it, so it was important to label documents for what they were. Just the other day, I went through and completely changed my project. Labels are now Plot Threads, which is working out exceptionally well. The book I am currently working on has nine primary plots all woven together. This is not an unusual situation for a novelist to be in. You have two things to keep very close track of: Continuity amongst plot threads, and how well those threads (even though disparate from one another, at times) feel together as you read the woven narrative. It makes your job so much easier to read your book in two different ways. Clones are one way to solve that, but I actually prefer Scrivener’s fluidity on this count.
Labels are perfect for this. If I want to review the continuity of a plot thread, I can simply search by Label, select all, and Edit Scrivenings. Save the search and this view is one double-click and a few quick keystrokes away. Keywords would be just as simple, but I rather like the colour based identification. I can glance at a chapter in Outliner (or Corkboard if I have pins turned on) and see which plots are represented, and in what order. I cannot do that with keywords.
But, this ability creates an information system which is very, very near to ideal in my own opinion. It combines a static hierarchy with a fluid “lens” or “scope” of viewing, with the ability for these lenses to be semi-crystallised via saved searches. With clever usage, this combination of tools can get around 99% of the situations which require clones.
Your point about using Notes for important top-level information is true. Though the ability to have the Inspector open in all modes does help a bit in accessibility, that information still requires a degree of scanning to retrieve. Using the keyboard to fly through a list of documents in Outliner, you can get down to your Notes really quickly. Note the Inspector also updates to reflect your current position in an Edit Scrivenings session, too.
There are five forms of meta-data that can be used for top-level data. Document Type, Synopsis, Label, Status, and Title. The last depends on your usage of the title. I use it for meta-data and define my titles in the narrative itself. If you use it as a literal title, its extra-curricular uses diminish. Given this knowledge, you can probably get everything you need somewhere in the top-level of visibility. Out of that list, Synopsis is the least visible, and Document Type, and Title are the most visible. It is for precisely this reason that I use the Title field for more than just the Title. It is a universal.
Least accessible are Annotations, Highlights, Notes, References, and Keywords. Each of these require access to the document to view; and access to the Inspector for the last three.
I am definitely still evolving my usage of Scrivener, and Beta 3 is going to bring along some new abilities that change this yet again. Highlights are getting a huge boost, and Annotations will become searchable on a selective basis.