At the airports I've done this, they are separate checkpoints. e.g departing Australia for the US: 1. check in with the airline using your US passport. If it is

At the airports I've done this, they are separate checkpoints. e.g departing Australia for the US: 1. check in with the airline using your US passport. If it is the return leg of a flight from the US, you probably put in your Australian passport details when booking so you may need to go through an agent. 2. go through Australian border control checkpoint, and show your Australian passport 3. board the plane showing your US passport if asked for ID.