I have a ms sidewinder FF, and can use it fine with my usb ch pedals.
Just go into the joystick area (where you assign joystick axis').
Click on select joystick
Click on rudder in the left most box (the one that says ah control)
Select your rudder pedals in the middle box (in my case CH pro pedals usb)
Then select the axis for the rudder (in my case X-axis)
If you have toe brakes, you can set them up hte same way, Y being left brake, Z being right brake (I think).
If you can't pick your rudders in the middle box (labeled joystick), I'm not sure how you set them up.
Also, make sure that the twisty motion on your sidewinder isn't assigned to anythign (unless you do want to use it for something).
If anyone would like some screenshots of these steps, let me know and I'll post some.