Controllers controlling multiple windows during multiplayer

[Queso_Fresco]

Like many others apparently, i can't seem to get multiplayer working for playing with Quetzal. I have each file loaded in its own window, and my keyboard can control whichever window is active, but the Xbox One controller I have plugged in controls both windows simultaneously.

I've seen a couple threads here and on Reddit about assigning controllers to different instances? But I have zero clue what setting that is. Any help is appreciated, thanks!