Audyssey can be wrong, but it often designates speakers even close to full range as "large". However, you should still set them to small (its the better option, but it is optional, and its Audyssey's recommendation). When you go into the manual settings, after setting up Audyssey, and change the speakers from large to small you will then also have to pick a crossover setting (80 is recommended, but you have choices). When you do this, all the Audyssey settings remain, but now the Low frequency effects are being sent to the subwoofer only, and not the speaker that was previously set as "large". Audyssey reacts to any changes you make in manual and you do not have to run the Audyssey setup again.