For those interested, I may have found the answer on p. 103 of the operator's manual.
If one wants to run conventional, command or both, use the variable voltage channel on the TIU.
So, I guess that if you hook up the TIU for the DCS Remote Control Set and run a Postwar Lionel engine, you run it using the MTH Z4000 like you normally do, and the DCS set has no impact on it. Then, when you run an MTH Proto 3 locomotive using the DCS Remote, you turn the power up to 22 volts on the Z4000, and run the engine using the remote.
Is that correct?
Arnold