Manually tuning subwoofer without Yamaha YPAO

On the subwoofer, set the X-over to Bypass.
Next set the subwoofer X-over in your AVR OSD, then adjust the subwoofer level as I already advised previously...

Just my $0.02..

Which Yamaha receiver? Some you can copy the settings of the Auto set up and then make adjustments.

If the speakers are set to Small then the subwoofer X-over in the AVR is also set. Now adjust the level for the subwoofer starting @ 0dB (AVR indication) with the level control on the subwoofer @ about 50% rotation.

How much bass output from the subwoofer do you have?
a. Too high?
Decrease it lower in the AVR's OSD
b. Too low?
Increase it higher in the AVR's OSD

As I mentioned previously you want to find a subwoofer level adjustment point which is not too boomy and not too little bass.

I hope that helps..

Just my $0.02...

I would advise using test tones with the spl meter so you can dial it in properly.

The subwoofer handles the LFE track plus the low frequencies from all channels that the speakers are set to Small.
Try setting things as advised, lets find out How it sounds..

Just my $0.02...

Don't worry about messing with your settings. You can always reset them and run YPAO again. Doing it manually does require some equipment. A 1/12 octave (or better) RTA would be best but you can do a lot with an SPL meter.

What are your speakers/sub and where are they placed in the room? Where is your seating?

Some basics, set the crossover on the back of the sub to its max position or bypass if it has that option. Sub at 1/2 volume on the back is a good place to start. You are using the crossover in the 3900 so you don't need to have a second crossover in the sub. You don't want to double up on the crossovers slope.

Good acoustics starts with location, location, location. Do the best you can with these. I know not all rooms are dedicated rooms and some compromises have to be made.

1. Seating location - Not against a wall or in a corner. Even moving it out a foot from the wall makes a difference.

2. Front Speaker location - Not in corners, close to the same height for the front 3, if freestanding speakers not too close to the walls, if on shelves bring them to the front of the shelf or TV stand. Aim speakers at the center of audience area. There may be more suggestions but without knowing more I can't make specific recommendations.

3. Not in a corner unless using a wimpy sub and need the output or using multiple subs for cancellation of room modes to smooth out the response. A safe bet would be between one of the front speakers and the center speaker against the front wall. A little experimentation is needed.

Run YPAO and put the mic on a tripod where your head would go. Don't rest it on your seat. If the sound is blocked by the chair (surrounds or backs) raise the level of the tripod so the mic has clear line of sight of all speakers.

If you have an SPL meter I'll go over manually doing it if these tips don't help first.

Natural - Is typically the best and most accurate choice.

Flat - Raises the high frequencies to make the sound flat at the listening position. Since high frequencies naturally roll off starting at 6-8khx in normal rooms and are a few or more decibels down by 20khz. So natural is the correct setting if you have accurate speakers. Flat will accentuate things like cymbals, glass breaking, and other things in this higher frequency range. Some prefer this especially if they have some hearing loss in high frequencies. It might get fatiguing after a while for others who don't though.

Front - A good option to use if your speakers aren't very accurate but you love your speakers. If YPAO is using all 7 filters per channel in its natural or flat settings it might be over EQing and I would try this setting. Too much EQ can be a bad thing.

No auto EQ (YPAO,Audyssey, ARC, MCACC, Etc.) beats a good audio calibrator but if everything is set up correct they should at least improve the sound. Since these things tend to be run in not ideal set ups they are often tricked and their correction does not always sound better.

Took me about 5 hours with Avia disk, SPL, and two subs. Almost perfect, but the SPL isn't at certain Hz. There was a correction table posted years ago for the Radio Shack units, digital and analog.

I can see why YPAO is messing up. Because your couch is against the wall you are going to be in a peak area for standing waves in your room. Because your sub is in the corner you are maximizing the volume of those standing waves. Can you move the couch out from the wall a foot? Can you move the sub to a better location?

I have my two subs acting as stands for my front speakers, works well for me

If you can't move anything you will probably have some boominess to your bass. To set your levels run YPAO first. Write down the sub distance. To set your levels get an 80hz test signal and set all your speaker levels and the sub level using this test tone it with an SPL meter.

"Are you saying that home theater rooms shouldn't have ANY furniture against the wall?"

Yes, I'm saying if you have it against the wall it is not going to be the money seat. It is not a good acoustic location. It sounds like the error you are getting is due to the sub being too loud. These microphones are not precision instruments and their measurements and EQ algorithms can easily be tricked.

There are standing waves that happen in a room and they will always be peaked near a wall. These waves exist no matter what (can't change physics) but placement of the sub will determine how much these standing waves are excited and how loud they will peak. Placing a sub in the corner excites the bass energy as it reinforcement from three surfaces (floor and 2 walls).

So you have a double whammy, seating near a wall where bass will be loudest (actualy corner would be a little worse) and sub in the corner where you are getting maximum bass output from the sub. Your standing wave frequencies will be peaked and the other frequencies are also at their maximum. You have too much bass energy and the receiver can't compensate for it.

I recommended you use an 80hz test tone for setting levels as that is your crossover point. You also want the phase of your subwoofer and mains to match at the crossover frequency. YPAO usually does that pretty good even if the subs distance measurement doesn't seem accurate, this is what sets its phase. It is compensating for phase and delays caused by subwoofer amplifiers. When you use standard pink noise it plays it plays all frequencies in that range and if your standing waves are peaked it is going to have a high SPL average and you don't have enough room to cut it down in the receiver without turning your sub volume way down.

The best you can do is run YPAO and hopefully it knocked down the standing waves a little with its EQ and then set your levels with a test tone at your crossover frequency and not pink noise or with YPAO. Hopefully, you don't have a standing wave at 80hz. You can get idea of what your frequencies standing waves are and what dimensions they affect by downloading one of the many room mode calculators available. Harman has one I think. If you happen to have one at 80hz then set the crossover to 90hz and try that.

When you say you moves the mic away from the speakers and seating where did you move it? You might still have too much bass energy with a sub in the corner.

Hope this helps.

There are discs with test tones on them. You can download one here but has a 10 second limit. Either make a CD out of it or connect your computer to your system. You want to make an 80hz sine wave.
http://www.audiocheck.net/audiofrequ...r_sinetone.php

If you want a longer one you can try here and pay about $7. Use the setting that says tone.
http://www.wavtones.com/functiongenerator.php

Here are some 30 day trials you can try. I haven't tried either of them.
http://download.cnet.com/Test-Tone-G...-10070156.html
http://www.esseraudio.com/test-tone-...st-factor.html

There might be some free ones around. We have a signal generator we use as part of our TEF measuring system.