Matt-
Look at the inputs and outputs on the TIU. For a command-only track, connect your transformer wires to either Fixed Voltage IN1 or Fixed Voltage IN2, and then connect the wires to the track to Fixed (DCS) Out1 or Out2 as appropriate. For tracks where you want to control the voltage (variable), connect wires to Variable Voltage IN1 or IN2 from the transformer, then Variable (CONDCS) Out1 or Out2 to the track as appropriate.
-John