Vortex, youre just looking at it the wrong way up

. You need to select the *controller* first, then the axis and then the input.
Select the controller (like your CH stick) i upper right dropdown box. Then map the X and Y axis to roll and pitch. For that, click on the axis and MODIFY (or double click), then select analog input and OK.
To map the rudder to the pedals, youll need to change controller selection in upper right corner. Choose pedals there. Then highlight the Z-Axis (of the pedals!) to Yaw (Rudder). CH pedals also have a X and Y axis (different then X and Y on your stick!!!) - those are the toe brakes. You can map those to "brake left/right" under analog input.
If you have trouble, shoot me a mail or PM and/or hunt me down in the TA... ill talk you through.