I have a 45CT-3 which I believe just a more powerful version of yours.
In AUTO mode, I set the small dial to indicate ISO and the large dial to indicate aperture. Then set the camera accordingly.
In MANUAL mode, I set it to either M, M1/2, or M1/4 which would be FULL power, 1/2 power, and 1/4 power.
The small dial does nothing. The large dial adjusts the output - that's it.
If I set it to W mode, it's the same thing as M1/16. For smaller power, it recharges fast enough that I can use it with a Winder.