I'm not sure how that would work actually... If the joystick is plugged in and configured, I would imaging it being the controller for the whole game, and not just for flying... I spoke with Raptor (a former member) about it, and we've come to a simple conclusion... You don't get enough flying time in the game to really make use of this... I'm not sure how many people here could help you with this issue, as it seems you are having issues with getting the game to use the stick properly... You might contact EA support for some advice... Perhaps they've tried it before? Sorry I couldn't be of more help to you. :-/
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