whats up

i finally took my 05 enthusiast in to the dealership because for a noisy throw out bearing, a clunking sound when shifting from first to second and a little grind in third gear. after they diagnosed the problems i was told they would have to replace the tranny and the throw out bearing. A few days later when i picked up the car i saw that they also changed my flywheel and pressure plate.
now for my question (i tried searching the forums for this but i didn't find anything): Is there a way to properly break in the new transmission?
thanks for your help