All joystick etc settings are now in the game.
Start the game,pick a plane,hit fly,pause the game.Right click with the mouse,a 'spanner' icon will be in the left top corner,click on that.When you open the menu for controls,scroll down until you see (for example) 'yaw' double click on the box,move pedals.
Same for the other controls,double click on an empty box,assign,and save to your profile.
Sounds more compicated than it is.
Thats about the gist of it I think,but I could be a bit mistaken,as I do it now without thinking about it!