Your Hobby shop is incorrect. For flaps to operate the servos must be oriented in the same direction if using a Y harness. The shop would be correct if you were installing the servos on the ailerons. For ailerons you want the two control surfaces to move opposite each other so the servos must be oriented opposite from each other. For Flaps you want the surfaces to move the same direction so the servos must be oriented in the same direction.

This is all contigent upon the fact that you are using a Y harness, and not using your radio and assigning and reversing spare channels. If you are doing this with the radio programming you mount them however you want and reverse the channels as necessary to get the proper control surface movement.