Well, that's one of the problems of working in 3D. Unless you're making something intended to play back on 9 HD monitors, you can probably scale everything down.
I'm with Dave in that you could scale your whole scene down. Parent everything to a null object and just scale it down. You can use a different lens on the camera and voila! Everything will be in the same relation to each other, but the scene will be much more manageable.
You can use the custom camera view and the camera tool to pull way back to see your scene. Personally, I would never put that many layers that far apart. I would put a wider angle lens on the camera or I would animate the scale of the layers as well as the camera move.
Think of the AE stage as a real world stage and pixels as inches or feet. Setting up a camera move on a real set that had your characters a mile apart would be more than difficult and way out of scale. Even if it were inches, 5000 inches is about 400 feet. Rethinking the layout will make things a lot easier.