your back foot should be right over the back fin for maximum turning effectiveness with thrusters.... (quads are not that critical as far as placement goes, but should be in the general area).
the pad should be placed so the foot is over the rear fin when on or against the angled kick part of the pad. put your hand over the rear fin location on the deck, and imagine that being your foot. then mark the location and put it on. simple right? if yours is not in the right spot, consider getting a new one put on correctly, and thank me later!!