Also a brand new user, so figuring things out and experimenting along the way. Pardon my musings but here’s where I am right now:
As of now I’ve been separating notes in a loose folder structure based on Zettelkasten: Inbox (Fleeting), References (Literature), Evergreen (Permanent), and a fourth folder specific for MOC’s (Index). As of now the Index has mostly been redundant cause I don’t have enough notes in my Zettelkasten to make it useful to form robust MOC’s. The only note I have in my top level vault layer is a “+Start Here” note that is the entry point to both the master index (or the index of MOC’s) and my actionable projects that I’m working on. This lets me collapse my folders to give a clear interface and starting point.
I don’t think mixing MOC’s with the rest of your notes is the right idea, because while you can manage organization through links and tags I feel like a flexible folder structure works best for both the visual aspect and separating not by topic but by level of processing for the note (fleeting->literature->permanent). Separating MOC’s from the notes they consist of makes a distinction that MOC’s are not a folder hierarchy aimed at shoe-horning the notes into categories, but an entry point for links to your notes. For now that works for me, but I’m excited to see how it will look at scale once I’ve built out my Obsidian vault a little more.
Some other alternatives I’ve seen and haven’t tried yet: adding symbols to the title to signify MOC’s/note type that organize by syntax, Johnny Decimal numbering (seems too top-down hierarchical for my taste), #MOC/topic nested tags, and even like you said total anarchy of zero folders (my Evernote trained mind can’t handle that much change!). Hope that gives you some ideas, would love to hear an update on what ends up working for you.