This game is mainly designed with VR in mind that the VR mode is is plug & play with not much configurations required, but as a throwback it's not really optimized for common controllers.
I suggest to configure right analog as cyclic X and Y, left analog Y axis as Collective, and left analog X axis as pedal at 'General', and then bind trigger button as Gun trigger axis at 'MD-500 specific', and handle the rest with mouse.