I’m still in the process of adapting my folder/tagging system to iA Writer from a mix of Ulysses (groups) and Bear (tags). When I first moved to iA Writer copied over my Ulysses groups and wrote a script to turn my nested Bear tags into a nested folder structure.
Since then I’ve ended up reducing the number of top-level folders, to make it easier to navigate (particularly on iOS). I’ve also decreased the depth of nesting. Now it’s basically limited to two levels, and most second level folders (folders inside of folders) are “archive” folders of one sort of another for files I want to keep but don’t need to touch very often. All of my working files are in the top level folders.
I’ve pruned back my tag set quite a bit from what I had in Bear (and gotten rid of all the nested tags since iA Writer doesn’t support them). Now tags are pretty much entirely orthogonal to folders. For instance I have a #draft tag that gets used across folders for various writing projects. Clicking on the tag in the sidebar will get me the drafts for all projects, or I can use the filter feature to find all of the drafts within a single project folder.
Finally, I’ve been relying on the quick search box quite a bit to bring things up. That’s usually my go-to way of finding a specific document.
I haven’t really made much use of favorites or smart folders so far. I’ve got one smart folder called “All” that shows me everything and one favorite folder called “Temp” that I use for ephemeral notes.