I'm running a cougar with saitek pedals, so I'm not sure if it all works in the same way, but it should do I think. You need to go to the controls section. on the drop down menu at the top, select "axis commands" or something like that. You should have 2 columns, one for the rudder pedals, and one for the joystick. Now it will probably have tried to assign some of the controls, but got them all wrong. If you highlight the assigned commands, one by one and click "clear", you will be ready to start again.
What you need to do now, is double click the command you want to assign and a box will pop up. You then simply move the axis you wish to assign and it will pick it up automatically. Go through all the controls with the same process and you should get all the basic controls assigned no probs.
While you're at it, you might want to tune the axis on the x and y of the joystick, or it will be ridiculously sensitive (it is on the cougar anyway). I set the axis curve to about 20 and it feels great......