If you do a search here in the forums for “add a new mode” you will see this informative FAQ by @JDRoberts
So think of this smartapp as a thermostat for automatic control only. If you don’t want automatic but want to override like in your example just disable the auto control.
But in your case you stated above yes the automatic will take back control on the next change in temperature at the sensor. If you want to increase the fan speed just lower the setpoint temp and automatic takes over at the new setpoint.
Hope that helps. I think I cover all this in the user manual that is built in to the smartapp? But if not it might be good for me to add it