Major,
In order to get the throttle and joysticks to work in AHII, you have to tell AHII what CH Control manager device works what controls.
* Go to AHII offline
* click on "Setup"
* Click on "Controls"
* Click on "Joystick"
* Click on "Select Joystick"
from this menu you tell AHII which control manager device you want to work which controls. Your rudder pedals may be device 2 or device 3, depending on how things loaded. On rudder pedals, left and right = z axis, left brake = x axis, right brake = y axis. FIrst, you highlight "rudder" on the far left. Next, you highlight one of the devices from the center column, and then you highlight "Z axis" from the right column. Now move the rudder pedals and see if the Z axis values change. If not, select a different device from the center column and try again. When you get it right, set input and then click on apply. Your rudder pedals will then work in AHII. Be sure to set up the brake pedals, you paid for them. Also, I believe that the Throttle on your pro throttle is the Z axis as well.
Salute,
PapaFox