The original TMCC consist programing only allowed the front and rear head lights of the consist to function. Atlas I believe has the Head light and rear marker lights on the A unit wired together. If there is a rear light on the A unit it also would be wired to the front marker lights if there are front markers. At least that is the way my Atlas GP7 is wired. I don't know how your B unit lights are wired. but programming for the center B units all lights would be off. Does the rear B-unit have a front and back head light? If it does when running in reverse the rear head light should be on all others off.
Front A unit TR ## Eng ## F set Front head light on in forward, off in reverse. Front coupler works but not the rear. A unit rear head light circuit does not work in the consist.
Middle B unit TR ## Eng ## set (all light off) (both couplers off)
Rear B unit TR ## Eng ## R (DIR possibly) set. Rear head light on in reverse, off in forward. Rear coupler works, front coupler does not. Rear B unit front head light does not work in a consist.
Most likely the marker lights are hooked to the same circuit as the opposite end head light.