If you start with a Helo airborn in a mission, you have to make it player controlled if you are in the FFG in order for the FFG to be able to control it via the ASTAC station.
In terms of the player helo being airborn, in order for it to be made a player helo, it must be airborn in the mission design, so not it is not possible to create the player helo on the flight deck of the FFG. However, you can have it start low on gas and needing to land and refuel. This can be tricky on the FFG, so maybe you can have a nice flattop around if you deside to do that.
So more crafty experienced mission designer can correct me if I'm wrong.
