To be clear:
With a joystick that is not a really fancy one(X52, CH etc.) You simply plug it in, and then in FSX you go into the options menu and set each axis control(throttle, flaps etc.) to an axis on your joystick, and actions to buttons on your joystick.
Doing it with the SST software is separate, and means that the conversion from 'joystick button' to 'action' happens outside FSX. DO NOT set both. Because it will get very confusing and it might not work properly.
I fly through the valley of death, but I fear no evil,for I am at 80,000 feet and climbing. Let's powerdive and scare that poor soul in that Ultralight there.