Hey James!
I'm also very interested in this. I have a n52 Speedpad as well and use it in the game. Unfortunately I haven't found a way to save settings directly in the game either, instead i map the keys in the n52 software.
This would have been all right if it haven't been for the fact that I can't find a way to map the throttle to the mousewheel of the n52 instead of the throttle on my joystick (MS FFB2). If anyone have succeeded in this please let us know!
/Jompa