The side to side movements you noticed behind a vehicle could be from the turbulences.
If you go to airtab website, they model the wake / airflow behind a truck as rolling -erh- tornadoes comming from one side after the other...
As far as I understand, vortices are used to virtually extend a surface, so that the laminar flow keeps going after the surface has ended.
[I may be wrong but i'll keep going
]
Behind a car, like a spoiler, it avoids having the laminar flow from wrapping back down on the trunk. It creates an air hole behind around which the laminar air flows, hopefully to meet gracefully. The goal is for the virtual shape of car+hole to be similar to a teardrop.
Between parts of the vehicle that don't have a nice laminar flow, the vortices can help the laminar air skip from one surface to another. This creates an air depression, but avoids the laminar flow to just hit the next surface head on and break into a massive turbulence.
So in conclusion, you could try to use vortex generators to replace your failed attempt to do a spoiler on the top of the cab. With some luck it could extend the airflow past your bed, and so that's where you want your tuft.
What to expect IMHO:
The tuft will shake severely and fuzz where the airflow contacts the bed cover. Before that the tuft should be not moving or moving slowly randomly. If you achieve laminar on your cover, they'll line up, but that's unlikely, even with the vortex generators. Instead I suspect you'll see all the tuft move lazylly around as they would all be in the quiet air bubble. The laminar flow should be around that bubble.
The only exception where I'd expect turbulence is where the sides of the bed, where the air probably would enter wrapping around the sides.
The bubble should become a virtual bed cover like the wood one (I think) you were thinking of putting which slopes down from the top of your cab to the end of the bed.
and I now find myself needing to do some tuft testing. All the photos I've seen are of tufts a good 6-8 inches long. Well, I have to define a laminar/turbulence area about 6 inches wide so I need to know if anyone here has used tufts less than 6 inches long. I really don't want to tape several dozen pieces of fuzz on my truck needlessly if they won't work. 
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