I have the USB Fighterstick and Pro Throttle, but the concepts are the same.
Each has 16 buttons (some buttons being positions of the 4-way hat switches), which appear as Button 0 through Button 15 on the right hand side of the Joystick Selection dialog. First task is to figure out what id the hardware reports to the software. The WinXP game controller calibration screen shows the number of each button pressed, except the numbers shown there are offset by 1.
Next, you bind the "logical" controls in AH (the list on the left hand side of the Joystick Selection dialog) to the "physical" controls on the devices. AH gives you 32 buttons: B1-B32. In my setup I have B1-B16 on the Fighterstick and B17-B32 on the Pro Throttle. Since both sets of buttons have the same id, it's real easy to link an AH button to "Button 5" of the joystick when you thought you were linking it to "Button 5" on the throttle.
Final step is to map game functions to the logical controls, which it sounds like you have figured out. I found it helpful to have a diagram showing which hat switch positions correspond to B1-B32.
Hope this helps! It took me an afternoon of experimentation to finally get my controls set up, so I feel your pain.