cortex-joystick problems

We have been working with the VEX robot set and we recently discovered that the MIcro controller and the cortex are a bit confusing. Most of the buttons on the Micro controller are not linked to the ports on the cortex. We checked to see what happened when we plugged the same motor into each of the ports and many of them are working for the left and right joysticks and not for the sets of buttons and triggers. If you used the button 5 on the controller it runs the motor plugged into number 6 on the cortex an does that with everyone you plug in 9 but you hit button 8 to run it