From the main ArmA 3 screen
Select "Configure"
Select "Controls"
Select "Controller" from the top of the window.
View the joystick is selectable, and customizable.
Set some controls with the joystick
Loading into a game...
View that the controls set at the start screen still work
Select escape from the keyboard
Select "Controls"
Select "Helicopter Movement" from the dropdown list
Attempt to set any one of the controls via the joystick does not work.
Select the "Controller" button.
View that the joystick is no longer registered.
Exit the screen back into the game.
View that the joystick no longer works for the given vehicle.