I set up my DEVONThink file system just like my paper one. Folders in a single DT database one layer or at most 2 layers deep. I name the folders appropriately by subject and they show up on my system in alphabetical order. When I last looked at Evernote there was a limit on the number of folders you could have. If that has been removed then it's easy, just create a file folder the same way you create paper folders and store the documents in side them.
Oogie McGuire - Mac, iPhone & Omnifocus
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Paonia, CO USA