Joe,
I noticed in the first pic that you have a Lionel IR device in the corner. I never liked the fact that the device came mounted on a base that, IMHO, detracted from the realism of the accessory.
If you like to solder, the device can be disassembled so that the base can be mounted underneath the layout and only the IR cabinet mounted on the layout. The only hitch is that the wires between the cabinet and the base are not long enough to reach between the underneath and topside of the layout and have to be extended by a couple/few inches. Since the wires run through the layout, you have to solder in place.
The only other issue is that the cabinet will probably not be tall enough for the IR sensor to pick up the body of a moving train and you will need to build a small base for it to sit on. I made mine out of sheet styrene.
See bottom of pic.