Jolly,congrats on the stick,I use one and like it most of the time.
I do not know how to program them,but the 2 "WHEEL" hats on your throttle can be programmed in the SST programming software,but I just dont use them,well yes,it is because I dont want to hassle programming them,but dont really need them right now, there are some that do..And you are right,you WONT see those "WHEELS" in the game,they can ONLY be programmed through the SST programming,either as an AXIS or as BANDS..
The mousey mover thingy-jig-a-ma-bob is not useful for much as far as I am concerned,and I do believe it can be programmed,but you wont see it in-game either..
The small button next to your mousey cursor mover IS in-game,and you will find which button it is if you press it,and make it whatever you like..
do a search for x-52 profiles,there are a lot,and you will get a taste of what it is to program the stick,and just what it can do..many people dont like it,but I like it alot,thats why I wanted it,so I could have more buttons programmed than I could remember..
Have fun with it..
Falcon23