command control remote switches

You connect the transformer to the TIU, and the TIU to the track.  Connect the Legacy controller to the outside rail of the track directly, do not run it through the TIU.

If you can run Legacy locomotives on the tracks, I can't imagine why you can't program the command switches, that's all that should be required.  Do the Legacy locomotives operate properly going through the command switches?

Perhaps you don't have a sufficient ground signal, try connecting a wire from the ground prong of the outlet you have the Legacy connected to, and laying that next to the command switch you're trying to program.

I think I figured out the reason. I am using a Z-4000 MTH transformer which seems to work inconsistantlyh with the fastrack command control switches. When I hooked up my inexpensive Lionel trtansformer to the track the switches worked well.

That's certainly interesting, I wonder if anyone else has seen that?  I have tested them with the PowerHouse 180 brick through an MTH TIU, the KW and 1033 transformers, and none of those environments had any issues with multiple command switches.