Glad to hear you got your new toy working!
You can use a fixed voltage terminal on your transformer to power the Flagman if your transformer has any. If not, then another transformer can be used to power the accessory independent of the track power. What transformer do you have?
If your transformer has fixed power terminals, then just switch the wire from the Flagman that goes to the track terminal of the transformer to one of the fixed voltage terminals on the transformer. The rest of the wiring remains the same.
If your transformer does not have any fixed voltage terminals, then another transformer would be needed. You could move up to a larger transformer that does have fixed power outputs, or get a smaller transformer with just variable voltage and hook up the Flagman to that transformer. With this set up, you can vary the voltage to the Flagman for optimum performance.

The exact answer depends on what transformer you are now using.

Larry