I have the X-45 and was feeling the same, just nothing like having those pedals underfoot

I used the stickworks driver set to create an entry for my rudder pedals (analogue CH pedals on my gameport) and made them joystick #2 in my windows gaming devices.
I then went into setup in AH, and selected rudder in the joystick setup, you have to be sure to select rudder, then choose the rudder on joystick #2, then either x or y axis will work (if you are using the stickworks drivers, which I recommend)and then be sure to click on "set" before clicking "apply" or AH will not keep the new setting, and will revert back to using the rudder switch on the throttle. That one had me going for a bit, until I caught on.
All in all it has been working just fine for me.