The first step is to unplug the programmer cable. This is the cable found on the right side of your device, and it'll either be a USB-C or Mini-USB cable, depending on if it's the older model or newer. The type of cable isn't too important, you just want to make sure that it's not plugged into the device while you're playing. Secondly, plug your controller into the A1 port. This is the USB-2.0 on the left side of the device.
After you've completed those 2 steps, you should be good.
Unplug programmer cable.
Plug controller into A1 port.
Alternatively, you can also just use Steam to launch your game and avoid all of these precautions. Don't be worried though, you won't get banned. The worst case scenario is that you'll be removed from the match, with no other penalties. Playing with the Cronus Zen is completely safe, and we encourage you to do so.
If you're playing on a console like Xbox, or PlayStation, it is not necessary to do any of this. You will be good to play however you'd like, with or without your programmer cable plugged in!