Relying on his YPAO is good advice for anyone who isn't really good at setting levels and such. However, he should double check the crossover settings for the speakers and subwoofer, as YPAO often gets those wrong, too often setting the main speakers to large, and too often setting the subwoofer crossover too high (of course, different Yamaha receivers have different versions of YPAO, and some may work better than others). He should also double check speaker distance settings, which he should be able to manage.
As for the needle bouncing around, assuming he is using test tones and not music, the meter must be kept perfectly still, or the needle will bounce around because the sound that enters the microphone will be different aimed in different directions, and he must be perfectly still while reading the meter, or it will bounce around, with many test frequencies. The reason is that sound bounces off of him, and if he moves, he is changing the way the sound is bouncing off of him. He should also have the meter at arms length away (preferably setting on something stable rather than in his hand), and it should be pointed straight up. He should not be directly in the path between any speaker and the meter.
Something like the inexpensive Sound & Vision test disc (retails for about $20) would be beneficial for him to see, which would also help with video adjustments. I highly recommend it; either you or he could buy it, and then loan it to the other one for setting up your systems.
As for his room acoustics, if he hears an echo when he claps his hands, he needs more sound absorbing materials in order to have decent sound. It is a common problem, and correcting it can cost less and make more of an improvement than most upgrades, assuming he does not have total garbage for speakers. It is likely to also make the room look better, if he uses a nice Persian rug and some beautiful paintings on the walls. Even a bookcase full of books will help. Basically, getting rid of that "empty room" echo by putting stuff in the room is beneficial.