Tivo,
Are you wanting the ditchlights to oscillate or simply have on/off control at each end?
If you don't need oscillation, you can use micro SMD LEDs and a simple four funtion decoder. If you wire each pair of D/L LEDs in series, you can wire each pair to one of the two spare function pads on the decoder with the appropriate resistor. You could end up with something like this: F0= headlight, F1=rear headlight, F3=front D/Ls, F4=rear D/Ls.
If you use rule 17 dimming, the headlights can be made to dim directionally. (my personal favorite)
The D/Ls could also be mapped to be directional along with being able to toggle them on or off using the function buttons on the throttle,
I installed front and rear D/Ls on an N scale GP15-1 like this and it works just fine.
Oscillation could be done but it would require either a six function decoder or two N-gineering ditchlight simulators.
I'm not familiar with the Atlas Gensets. Would you need to add the ditchlight detail castings as well?
Jim