Goto,options,controls,map controls.  It's as simple as pressing a button or switch and double click on the highlighted item then select the function.
  If you goto map keys you will see a virtual KB and the submenues will tell you the key press and functions.
  The basics should be mapped,pitch and roll and if you have a twist stick the yaw. to map rudder pedals,select the pedals in the input device,upper right and set up the yaw axis,same if you have a throttle,select throttle and map as you would the JS.
  It's very simple once you know were to look!    

PS: once you have your controls setup,save a copy of the settings folder to a zipdrive or a hosting service,I use Gmail and a zipdrive in case I cant find the zipdrive,then you can setup a comp in a few seconds!