I did. It came out with the speakers not the same.
Do I go in and make the Left & Right ones match each other?
Do you understand what YPAO does? In part, it sets the volume of each speaker so the sound reaching your ears, (the microphone position), is the same from each speaker.
There are many things that can make one speaker sound louder or softer than another. YPAO sends a known volume to each speaker, one at a time, then measures how loud the volume is at the microphone. It adjusts the relative volume in the AVR so everything is equal at your ears.
Assuming you followed the YPAO directions, and used your MAIN listening position as Position #1, I would not change any volume settings. At least not yet. If you do, you will be unbalancing your system. Perhaps that is your preference, but I wouldn't do it to start.
Now your subwoofer. YPAO set it at -6.5. In order to balance your system, YPAO had to turn UP all your speakers, and turn DOWN your sub. In a perfect world, all your speakers and sub(s) would be set to 0. Fortunately, you can help.
I think your sub has a volume/gain control on the back. You need to turn it DOWN ~6.5dB. (I know... you want more bass, but stay with me here.) Now re-run YPAO. Keep fiddling w/ the volume/gain on the back of your sub until you can get YPAO to show 0, or very near 0.
Now you have achieved the BALANCE between bass and higher frequencies that was intended by the artist and recording engineers. From here, it is a matter of your personal preference, AND you have maximum flexibility to change it up or down in your AVR.
Listen for a while and see what you think. Listen to music. Listen to big action movies. Many of us prefer the bass level to be as intended for music, but louder for movies. Perhaps you prefer louder for both. You can play with it, knowing you're starting from the intended levels.
One note: Your AVR has a maximum it can turn the volume of any speaker up or down. It's probably somewhere around 7-8dB. Use the AVR to adjust the volume within its limits. If you find you want more from the sub, you can go back to the volume/gain on the sub and turn it up a bit.
During your balanced, critical listening, you may decide you want the Left, Right, or some Surround speaker louder or softer. Perhaps your partner's seat is very close to one of the Surrounds and you want to turn it down a bit. It's OK. My point in all this is that I suggest you start from a balanced position. Change any volume you want, but only if you have a specific reason. Do not change something just so the numbers match.