I use the gas/brake pedals from a MS Sidewinder stearing wheel as rudders along with the TM FLCS/TQS joystick.
Go to "Setup" then "Joystick" then "Select Joystick." In the joystick window, select your joystick by clicking on it. Then click the "Set all Input" button, and "Set all Buttons" button. Now all your inputs and buttons will be set for your joystick.
Next select the rudder from the window under AH Control. Then select your wheel controler in the joystick window. Then move your pedals to watch the Joystick Input window to see what axis is moving. It is the Y axis for mine. Then select this axis. Click the "Select Input" button below. Click OK to return to the Joystick Window.
From the Joystick Window, select the rudder from the drop down box. Press the pedals and watch the movement on the graph. If it moves backwards, click the "Invert Axis" box above.
That should do it... nothing to it

Gunner