I have five top-level folders:
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Personal — Projects/actions in personal areas of life
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Business — Projects/actions related to my business
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Maintenance — Project/actions for keeping my system up-to-date (e.g. “Perform Morning Review” project) that aren’t specific to Personal or Business.
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Checklists — Checklists that I run through regularly (e.g. “✔︎ Prep | Teach Yoga Class”). I got the idea from @joebuhlig.
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Templates — Project Templates that make use of the Populate Template Placeholders script written by @curt.
Folders within these top-level folders get more granular. For example, within Personal I have a folder called “Friends and Family” that contains a single action list called “[Friends and Family]” (I’ve adopted a convention of including square brackets in the name of single action lists) and projects (e.g. “Plan Birthday Party for Kieran”).
I use tags to draw items from across the system based on what context they represent (e.g. Home or Shallow) and other attributes (e.g. Vacation for everything I want to get done before I go on vacation).
In a nutshell, folders allow me to focus in on specific areas of life and tags allow me to view related projects/actions across all areas of life.
I posted a free OmniFocus Workflows with Tim Stringer video that goes into my setup and workflows in detail. I plan to publish an updated version of this video once OmniFocus 3 is available on both Mac and iOS.
I hope this helps!
p.s. I’m also a big fan of Evernote (and an Evernote Certified Consultant) and make extensive use of tags, essentially as “metadata” that is helpful when finding information.
