It will actually go into the Batt/bind port. What you will do is plug the BEC into the 3GX and bind the 3GX/Sat/Rx(if you have this) to your Tx, and at this time, your BEC will be plugged into any available port other than the color coded ports. This should provide power so you can bind. Once bound, pull the bind plug, disconnect the battery (bec) then plug the bec into the batt port.
I am assuming you are only running satellites, but with what you stated about aux1/aux2, you might be running a separate Rx. Let me know if this is confusing as well as what your setup is and I will help further.