I have not wired up my Atlas uncoupling tracks yet on my new command control layout. Since I follow along with the train, I have the uncoupling track switch on the layout's edge close to the uncoupling track section. I also have done this with my yard/industry switches. Too much trouble looking for the control switches on the controller.
On my previous layout, also command control, I wired the uncoupler's screw terminal to the center rail of the track (through its switch), not to a transformer. Nobody has mentioned this so I was wondering if there was a reason for not doing this? I don't remember having problems with it.