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In Gmail, any items that are to become actions are marked with a star and left in the inbox until I grab the pertinent info with my quick keys and stick it in omni. Once it's being tracked I archive it and label it appropriate to its counterpart in Omni projects. Once the action is complete I unflag it in Gmail.

Items to be filed that are electronic are emailed to my evernote account. Inside evernote, I use an A-Z notebook system for filing and then label them for additional access.

In the physical world I use a combination of tricks. I do maintain a physical tickler -- a "43 folder" type system for those things that come to my desk that are not ready to be filed but need to be looked by a certain time and look at that every day along with my 4 physical inboxes. I have one for people who want to give me something, I have one for things I generate that I am not ready to deal with (close to my desk, whereas the other is outside my office). I keep an inbox at my home desk for things that are going to be dealt with there and I keep a 3 sided pouch labeled mobile inbox in my brief case.

All these inboxes source the both the physical A-Z filing system in my office and home, the physical tickler and Evernote (via scanning).

I keep a brother labeler and readily file folders for physical items, though most of that stuff gets scanned.

Finally, on my ipad, I dislike the keyboarding and take daily notes in Dan Bricklin's Notetaker HD, and then output them via email and Notetaker strings right into their home notebook in Evernote. Any item that I write in a red pen is deemed actionable when I create it and will source Omni. I also scan for action items when I review my notes the next morning and source Omni.

I feel a bit redundant in maintaining so many scans of paper that is in my A-Z system, but don't see a way of completely going all electronic and don't want to go all paper.