Can you adjust control throws in the real flight program when using the interlink controller? I'm also wondering if I use my own transmitter with the throws programmed in for field flying if it transfers to the real flight aircraft.

go to the airplane tab and instead of select airplane, click on the edit (current aircraft)option. Each control surface is link to it's wing. For example, if you want to change the maximium throw for the rudder, go to the vertical wing section and change the degree of deflection. The adjustments on your digital radio will work as well.