if you highlight the "rudder" on the left of the screen, you will notice the right window giving you options on what axis you want to run the rudder on. If you want CH peddle to be rudder..highlight your CH controller, highlight rudder, and highlight "Z" axis, then hit SAVE (or whatever they call it..im at work and can't check.) Your other controller should already be configured, but since you changed the option for the rudder to run on the CH, your "twist" on the evo is now not mapped to do anything. Now you can use both controllers at the same time. And no, dont delete the otehr axis's (dont think you can anyways) they are only showing the different axi's because it is basically asking you if you WANT to select x, y, etc. If you dont pick x or y, they wont be mapped to the CH.
When your done, stay in that setup window and move your controller j/s and ch peddles around. for the j/s you will see the x and y axis numbers going up and down. When you move the CH peddles, the Z axis numbers will go up and down. Oh ya, and dont forget to go to the joystick calibration in AH2 when your done