Daniel,
Wire it up normally and ad the wire from the Command base, "U" terminal, to the outside rails. Just leave the switch on the powermaster in conventional. TMCC is on all the time. So make sure give the powermaster an address, like "TR" 1. So when you turn everything thing on. First address the track "TR 1", turn the power up all the way, then address your TMCC engine, like "ENG" XX. Engine XX , which is TMCC will run like normal, in command mode.
When you are going to run your post war locomotives, you just have to address the track and then use your remote to run the train on that track.
So, I'm re reading your post... "extra transformer"? The powerbase and powermaster do not create power, they only control power, from a transformer or a PowerHouse i.e. PH-1 135 watt brick.
Attached are the instructions for the current PowerMaster, which will be wried the same as your older model, and instructions for a 135 watt power brick. Your trans former could be wired up in place of the PowerHouse.