Geoff, the 663 does have manual distance adjustments available for all speakers, including the sub, but that wouldn't seem to be the solution for your complaint about the sub level. If the sub trim level on the 663 which showed after calibration(either by YPAO or manually)isn't high enough to send enough voltage to keep the sub amp "awake", you should turn the level control on the back of the sub down farther(say about 1/4th of the way up)and recalibrate(the 663 will have to output more voltage to compensate for the lower setting on the sub's level control).
Then of course, the "thump" that you say that you're looking for may not be a realistic expectation. A sub shouldn't be heard as a separate source; the impression should be that it isn't working but that the other speakers are putting out more bass.
