I use OmniFocus for projects and next actions but track the higher levels through OmniOutliner. While it probably sounds a bit naff, i really like using narrow, colour-coded checklists that i can place alongside my main Omnifocus window: e.g. 20,000 ft. next to the main window through to 50,000 ft. at the other side of the screen. The downside of this approach is that i need to manually drag things around to get it set up; the upside is that it allows me to think about the various breaks and continuities that run through the levels in ways that i wasn't able to do when i was using a hierarchical structure within OmniFocus.
I'm also interested to see how others do this within (or in conjunction with) OmniFocus.
Can you post a screen shot? I am having trouble visualizing it.