Well every axis on the controller can be used as rudder, you have to assign the rudder function to the axis you want to use in the AH config panel.
Better use an axis that returns to center automatically for the rudder IMO, else you'll have to find the center manually every time you use rudder.
EDIT : I just understood what the problem is, you have 2 axis on the controller.
I don't think you can configure rudder right for the right pedal and rudder left for the left one.