Mark,
Think I can help. I have played around with CH products forever it seems and have both the analog setup you have as well as the digital setup(usb)(thanks in part to CH sponsorship of some events I won in Air Warrior).
First of all, understand that you have many options to program your devices. I won't go into that and will take you through the simplist route I know.
Second, programming your keys on the pro throttle and combat stick has nothing to do with the movement axes of the stick, throttle and rudder. Speedkeys basically allow the keys on your controls to issue one or more key strokes like your keyboard.Your calibration and support of the axes of your controls come through windows, and then through your game(yes, AH is a game!)
Here are the steps:
1. If you haven't messed around with the command keys in AH, that's good. Just make sure all the control functions you want are supported by command keys.
2. Download speedkeys from the CH site
www.chproducts.com Also download drivers for the combat stick.
3. Install speedkeys and the drivers. Driver installation, as I recall, is unzipping files to a temp directory and then right-clicking on the inf file with your mouse and then clicking on install.
4. Hook up your controls as recommended by CH.
5. Bring up your game controls through start/settings/control panel/game options and then select the CH option for combat stick/throttle/rudder combination (I can't remember all the details but experiment until you get all three devices recognized). As I recall, there was a selection for ch devices where you may not need to check the rudder box to get it recognized.
6. After you get your controls recognized in windows(calibrate and test), it's time to bring up speedkeys. I have come across instances where speedkeys would not recognize the presence of the pro throttle's programming chip. If that happens, let me know as there's a simple solution to that.
7. Make your initial control selections and then start programming. I'll send you one of my files but be careful as I use the CH force stick and the hat keys are reversed compared to the combat stick as I recall. If you take a look at someone else's template, you'll get an idea on how keys are programmed to issue repeat key commands(like firing) as well as some tricky stuff that can be made with the programming. You'll also get to see the illogical setup and thinking some of us have(hehe)in assigning keys.
8. After you've programmed your keys, it's time to go into AH and through setup, get your stick, throttle, and rudder controls recognized for their axes movement. Test your key commands out until they're exactly what you want.
If I've confused you or you need more detail, write me at jlopes89@earthlink.net. You can also call me too if you wish to waste your money.
Good luck!