Ideally, I would have them 3 feet or more from any side or rear walls, and 8 to 12 feet apart from each other.
Next is a matter of understanding the baffle step compensation. tHe quickest way would be to, after the above setup, run audessey with two or three test tones.
Now check what kind of boosts and cuts audessey has applied from 60hz to 500hz or so.
For example, if it goes
60hz - +2db
100hz - 0db
250hz - +2db
500hz - +1db
1khz - 0db
2khz - 0db
Then that probably means your speakers have some boost arond 100hz, but are too far away from the wall for the design of the speaker. And if it goes
60hz - -2db
100hz - -4db
250hz - -2db
500hz - -1db
1khz - 0db
2khz - 0db
then it means your speakers are likely too close to the wall. Now i'm not saying your speakers necessary have that 100hz boost. I don't know the frequency response of those off the top ofmy head. But you get my point... focus on that region below 500hz or so.
Move your speakers back and forth until you can get that boost or cut in the bassy regions to as close to zero as you can. Optionally, just let audessey apply its boost/cut EQ but then audessey has to be ON otherwise the speakers will not sound right.
Try to keep your speakers 2-4 feet away from the rear wall ultimately. This will give you the best possible stage "depth".
For subs, stacking them might give you a bit more max output but I don't recommend it.
The biggest advantage of multi subs is if you can get them across from each other on opposite walls, and as away from corners as you can get. Unless your smaller sub is actually intended as a mid bass module of some sort, I recommend running both subs with the plate amp crossover at the highest possible setting or OFF if possible.
Let your receiver deal with cross-overs. Trying to cross over a sub with another sub, and yet both are being crossed via receiever to 3-way mains..I can only imagine the issues you would run into.
Audessey is setting it to -12 because sending "-30dbFS" or whatever voltage to the subs would make the subs too loud and noticible.
Think of it like this:
Your Speaker Left/Right with a test tone voltage give you 78db
Your Sub with the same test tone voltage might give you 90db, even though it might feel the same level you have to remember your ears are less sensitive to bass frequencies. Trust the mic that this is actually this much louder than your speakers.
What audessey tries to do is match them. So (although it might be a bit different) it might cut the total volume by 3.
So the "standard voltage" will give your main speakers 75db and your sub 87db.
Now that means your sub is 12db louder. That is not desirable if you want balance... so audesssy will cut your subs down by 12db at standard voltage. This will mean the standard voltage will give your main speakers 75db and your sub 75db..."matching" them. It will still send more voltage to either the speakers or the sub if the content calls for it.
Now movies are generally mixed with a louder LFE channel.. up to 10db louder at the loudest moments. So the max of your mains might be 105db but your sub will still be asked to do as much as 115db. So the bass will be prominent when it wants to be, even though the speakers and subs are set to the same level. Let the recording handle how loud the bass should be relative to the rest of the signal. Don't fall into a trap of trying to get the bass to show itself. The best bass is so subtle that it's pleasant and forceful but you can't even tell your subs are doing anything unless you put your hands on them.
As the above paragraph suggests, sometimes people set the LFE channel to -10db because the sheer force of that channel can be disruptive. In your settings, somewhere or other, you might find an option to set it to 0db but don't confuse that with the level trim.
Back to dual subs. Because they are NOT the same subwoofer, you have an issue of gain-matching. Normally I would not recommend trying to mix and match two subs.
Unfortunately, the only way for you to match the levels of the two different subs together is with an SPL meter of your own. You need to send a 75db test tone or pink noise to one sub in isolation at its final location as I suggested above, and play around with its gain dial until you get to a specific number on an SPL meter. Probably 75db. Next you need to do the same for the other sub in isolation, at its final location. ITs gain dial setting will likely differ to get to that same SPL. Once you've dealt with the two subs, you need to run a Y-Splitter from the LFE-out channel so both subs are getting the exact same signal. You may wish to do the "crawl test" for one or both subs to find optimal locations on one or both walls, prior to doing the above.
After all the above, with the Y-Splitter in place, unless your Denon has dual DISCRETE sub outputs, you will need to next look at the phase dial on one sub or both. Because they will not be co-located, they will likely not be in phase when they reach your seating position. With one person sitting at a given seating position, run test tones through both subs at the same time with your hand on the phase dial. When it sounds most clean and loud to the person at the sweet spot, you've found the right phase.
I recommend keeping the smaller, weaker sub closer to you to lessen the amount you're asking from it.
run the auto-setup and see what you get.
Now for surrounds. I recommend getting them at least a foot or two above head height.
