From the Flying Giants forums, it looks like you got things sorted out. Generally, though, you don't set up a model in the student transmitter, just make sure the channel assignments, directions, and trims are set to be the same as in the instructor's transmitter. Set the Trainer system in the instructor's transmitter to FUNC for the channels you want to use. That way, any mixes in the instructor's transmitter will be applied when the trainer switch is pulled.
You can use either of the micro-micro trainer cords.