I'm writing this post for all of the wrong reasons. I've had this "write a post about pitfalls of org-mode," on my org-agenda for weeks, with a list of "ways I'm not doing things right in org-mode." One of those pitfalls, the main one in fact, was "you're living too much in the agenda view, and not thinking of your org-files as working documents and outlines onto themselves."
And because I'm living too much in the agenda view, I'm writing a post (that I need to write, but have been hesitant to write for a while) mostly to get it off my todo list.
This is certainly an acceptable way to work, and I think todo lists mostly exist in order for their items to be completed and checked off. At the same time, I've said (and I keep saying) the beautiful thing about org-mode is that it allows you to plan and process your projects in a way that makes sense for project planning without centering your process on "actionable items," which is good for doing things but less good for planning things.
And so I've been failing at keeping the "planning" and the "doing" as separate thought processes. Note to self: do better with this.
The second pitfall is in the "org-refile" functionality (C-c C-w), which allows you to send items and subtree's to other parts of your org-agenda files. I think part of the problem is that I don't really get how it was intended to be used, and as a result when I try to use it, it doesn't work. (I tooled around in customize, after I wrote this and found: that the following bit (in custom-set-variables) to help, bunches:)
'(org-refile-use-outline-path (quote file))
When I want to refile something, I think to myself "it should go to x file, under which heading, hrm... lets see what's there..." And my options are presented to me in [Heading]/ (filename.org) format. The problem is that org is thinking backwards from me, and as a result I end up miss-filing things, or not using the refile as much as I should because it doesn't really work for me. Hrm. Not sure how to hack this.
In anycase, back to working.