FWIW, I use the Finder (macOS … whatever the equivalent is in Windows) to establish and manage my folder hierarchy. I use Obsidian and other applications to create or manage document content within the folders at appropriate locations. I do not replicate folder hierarchies from the Finder level exactly also in Obsidian.
Perhaps if I was using only Obsidian to do everything, my approach would change. My course documents however contain a mixture across five or more different applications. Blending content output from some applications into Obsidian, ostensibly so that Obsidian could be a “Finder replacement”, is far more trouble than is worth the effort.
Otherwise, how you set up your folder structure is a matter of personal preference regardless whether this is for academic teaching or real estate management or small business operations. Here is a snapshot of mine for one course …
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JJW