Normally, when setting up a trainer system, you have the model on the ground and you flip back and forth between the master and student transmitters. You adjust the controls so that there is no control surface movement when you transfer control between master and student. In the air, if the trim on one is moved, the trim on the other will need to be moved, too.
We do suggest that the model be flown with the master transmitter first so that it can be 'settled down' before it's used in the trainer situation.