Probably with jscal-store and after reboot probably would need to reload them with jscal-restore.
//EDIT: If I recall correctly, for a joystick “js0”:
- save config:
sudo jscal-store /dev/input/js0 - restore config on reboot:
sudo jscal-restore /dev/input/js0
Now that has to be named the same over reboot so if you have multiple joystick this is where it can be tricky. but if you only have one joystick/controller, then it should work.