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In my Documents, I've set up top-level folders for my areas of responsibility, for example ...

* Sales
* Marketing
* Finance
* Personnel
* Activities
* Surroundings
* Well-Being
* Family

This structure matches closely what I keep in OmniFocus, and each of these folders contain various folders for projects or information. Then, I have folders for general app-related stuff, for example ...

* Curio
* OmniGroup
* Parallels

... as well as for general storage, for example ...

* Databases
* Literature

I use the labels feature to set Work, Personal, Application, and General labels (and colors) to the folders. This helps in list-browsing my Documents.