Basically it should be as simple as assigning the rudder to your pedals. I don't know if the mouse controlling system bypasses that.
You would think so. I didn't lose my rudder mapping. The toe brakes seem to work, but looking back when on the ground, the rudder doesn't move at all with the pedals. Sure does with the mouse, even though I only have mouse to control aileron. I tried a take-off with full left rudder pedal and as soon as I get off the ground it sure gets real squirrely!
So the rudder pedals work like normal in the air, it's just really counter-intuitive when on the ground, and as far as I can tell, there is no preference to get rid of this.