I agree, keeping both completely seperate is sort of rediculous. What I mean is that in my head, they're two seperate inerlocking tools. Left hand and right hand. What the organization needs to do, what I need to do.
Maybe this metaphor will help.
I own corporation XYZ and I hire a project manager. I still need to steer the company, but the project manager takes care of a lot of the details on certain projects.
I am the project manager, and I use GTD. I need to steer the project, but I also need to take care of the details of what I need to do, which is where GTD comes in.
It's the same sort of relationship.
This kind of thing is difficult because GTD is a way of managing your time and your actions, but when you're a project manager, you have to manage a lot of other things as well. If you only had to manage your actions, or only had to manage the project and could delegate 100% of the work to other people it would be easy.
But because you're given a red tool for managing projects and a blue tool for managing your time whenever you come across something, the choice between using the red tool and the blue tool is confusing. Some things are clear-cut, but other things could be either/or, or both.
"Revise subsystem B" is both a project task, which you've delegated, and something you personally have to wait for. You need to track it with the red tool to ensure the project is on time, but you also need to track it with the blue tool to ensure you personally don't forget about it.
Wouldn't it be great if there was a tool that could contain both, and you could simply add red and blue flags and it would appear on two different lists.
I think the answer would lie in keeping seperate project lists, and reviewing them regularly (project goals, personal goals), and keeping next actions for things you specifically can do.
These project lists would be one level of granularity below the MS Projects/Excel spreadsheet, as was pointed out before - no level of granularity on an MS Project can get every project on there. I would also reduce the granularity in MS Project and start relying on my lists for anything that doesn't fall into neat 8 hour chunks.
So 1. MS Project, 2. Goals Lists, 3. Next Actions.
One of the things that strikes me about GTD is that it's very time agnostic. Unlike MS Project, it doesn't care when things get done, nor does it care how long they'll take to get done. The only thing that's important is the order. If "A" has to be done before "B" then "A" is the only thing you write down or worry about.
This agrees with me more than MS Project style management where each item is timelined in a GANTT chart. Of course, GANTT charts are very good at doing things like predicting when dependancies will come up.
My personal preference would be to use MS Project for those dependancies and broad strokes, figuring out how long the project will take, and even planning the microcosmic substeps if you feel it's important to list every substep somewhere so you can track them.
But then use GTD/lists to ensure things are going well on a day-to-day basis, using the MS Project file for reviews.