Are you using the Atom to control a vehicle too or just for a gimbal controller? Did you know that your FC can do both at the same time? For that, the key is that you need more outputs. That is the same problem as if you want to fly an octocopter. On the Hardware page you must set the Receiver Port to also do output, and you will have to modify the cabling or at least make an adapter cable.
If you just want to use the Atom as a gimbal controller and not a flight controller, then you should be able to just use any 3 of the 6 outputs that are normally motor outputs.