Is your in-wall Klipsch sub a passive sub that works with your power amp? Or does it work off a pre-out from the Yamaha AVR? Always include specific model numbers of all gear, it often helps. Can't think of anything remotely current from Klipsch in terms of a passive sub so I tend to agree with sven's post. You will need to calibrate the avr/amp/sub, YPAO can do that for you or you can do it manually with other gear.