I've used the YPAO initially for setup but then refined it with the Radio Shack meter.
I've also had a couple of Yamaha receivers (RX-V2400 the current one) and found it necessary to boost up the center channel a couple of dB's for a more 'relaxed' listening level; the dialog on many DVD movies is just not audible without this adjustment.
I have an SVS sub and an adjustment is also recommended for this sub as well as many others. A quote from the SVS guidance on setup: "Because the Radio Shack sound meter is relatively insensitive at very low frequencies you'll actually be set several dBs higher than what's read." As a result of this suggestion I advanced the output 3Db's from my base reference of 75Db's and that worked out fine for the room acoustics.
-GeorgeM