I used Soundtraxx O Scale decoder for electric locomotives (TSU 4400 for electric locos). I also used a standard 8 pin connector to the Atlas board that is set up for the standard 8 pin connector though I used a bit heavier wires to the connector than usual considering the large Pittman motor in the model.
It was a very easy DCC install. As to the pilot, the body just needs to be snug down, perhaps a wire or something has snagged and prevented it from seating. It's pretty easy to remove the body. See the original Atlas instruction sheet.