To the original post. If I were ordering a new truck, i would order it with factory fairings to the back of the sleeper, from there I would likely use side boxes starting as close to the fairings as possible. If I decided to use a skirt, it would start behind the boxes and continue to the first rear axle. Built and installed correctly, there would be little or no loss of efficiency imo. Considerations would be taken for access to the generator or any other servicable component hanging fron the side rail. I would also want fairly easy access to get under the truck, in front of, the axles. This could possibly all be done with one removable panel on one side...including access to the generator.
At the rear, I would have skirts similar in appearance to what you see in the link Phil provided. You would have to work around the liftgate and liftgate controls obviously.
I would in no way have anything directly behind the axles that would block airflow behind the axles. Example: no toolboxes or solid mudflaps, etc. Once the air has made it to that point, its not going to hurt you anymore unless you re-trap it with something. If the liftgate still has air that could get to it, i would consider something that could mount to the highest point possible just behind the axles, full width of the truck, angling down and toward the rear as far as possible and serving to deflect the air down and under the liftgate. This is, of course, the same principle as the wedge type fairing mentioned above. You may need something similar, but yours would have to be custom built to work around and in conjunction with the liftgate. A flat piece of material installed correctly will divert air just as well as that big plastic wedge...imo.