First off, if you have the latest version of CH Control Manager, you have to calibrate your joystick within that program. The new version of CH Control Manager no longer allows you to use the Windows calibration applet and you have to now calibrate within CH Control Manager.
Next, start AH and bring up the clipboard and click on Options-->Control-->Calibrate Joystick and follow the instructions to calibrate your controls.
Next, click on Map Controllers and select your controller. You'll now see the axis for the selected controller. Highlight the axis (one at a time) and then click on the Calibrate Axis button and follow the instructions. Do this for each axis assigned to your controllers.
Now your controllers should be properly calibrated. Just a note, if you want, you don't have to calibrate the assigned axis for each controller. However, I do recommend that you do so to ensure that the controllers work properly within the game.
ack-ack