https://forums.robertsspaceindustries.com/discussion/110454/actionmap-and-controller-mapping/p1 ^ This post walks you through the steps.
I saw some forum posts where people were working on it. Pretty cool. I'm still not settled on a for certain setup but I'm still leaning toward left hand joystick and right hand mouse. I'm just waiting until things are a little more settled. Only bad thing about that is, I'll be really accustomed to M&KB setup by then =P I'm thinking joystick to fly, then release the joystick and use my mouse to fine tune my aim when in combat. I dunno how that'll play out, if I'll have to make sure to have my mouse movement extremely stationary or if the joystick and mouse will ignore the input of the other as long as I'm not trying to use them simultaneously. I know in Planetside when I fly, and with the Magrider, I control them and aim predominately with the mouse itself, then use my thumb buttons for quick analog movements.