This is what I have done RLeeds, I have the wingman rumble pro (considerable diffrent) but the setup should be just about the same (I hope!! )
Make sure your controller is plugged in. Open FMS and go to the Controls menu, click Analog, then a small menu will appear, it says No Interface, Joystick Interface, etc. I chose Joystick Interface (try this first, if it doesn't work, try one of the other selections) Then press Mapping/Calibration. Another screen pops up, the left half should be Mapping, the right half Calibration. Click Calibrate, the some of blue lines should start dancing, follow the instructions by moving your sticks around. The lines should be moderatly still. Click Next. Center your sticks, then click Finish. (Your not done yet! ) You need to determine which stick does which. Move your throttle back and forth, one of the blue bars should go up and down, substitute the number corresponding to that bar on the Mapping side of the menu. Follow the same steps for the other channels. If the channels are reversed, check the Inv box. I don't know what the Exp box does (maybe it's exponential, I haven't expirimented enough)

Hope this helps!!!