I am not familiar with newer Atlas F units. The older ones I looked at had solid diecast truck structues. The only way to change wheels is to use a sturdy wheel puller and pull the wheels off the axles and use a press to install new wheels, with one side insulated. Some trucks on some brands newer models have removable base plates on the underside. These can be removed with a screw driver, then the whole axle/gear can be removed and a new one dropped in. This is much easier than having to use the wheel puller.
In addition to changing the wheelsets, you have to design (or obtain Atlas) two rail pickups. Generally this means wipers on the insulated wheel side and uninsulated side passing pickup through the truck body. The wires from wipers would be similar to the wiring from a center rail pickup.
So the bottom line is that if you don't want replace the unit, the easiest conversion is to replace the shell. The hardest is to replace the wheelsets on the current units.
P&D had lots of parts to install their drive. Going this route would mean replacing the entire mechanism. The good thing is that you use the existing frame and shell, but it takes a little work to install new body bolsters and motor mounts. These are great drives, but are totally different than the motor on truck type in an Atlas unit.