Well, given that you guys are obviously the ones to talk to about this, I suppose I need to give a little more insight into my exact situation so you know why I'm asking to begin with.
Here are a couple of picture of my living room where I am setting this all up as well as an updated pic of the work I had to do to the mantle to get the new center channel speaker to fit. The mantle has since been completed and painted as of the time this pic was taken.





The speakers shown in these pictures, except for the last picture of the mantle, are focal's. They are bookshelf speakers that I recessed into the wall when we got the tv set up over the mantle thinking that was just awesome.

After having the Focal's for some time, it became more and more annoying that sometimes I would have a hard time making out voices, etc. and the 8in sub that came with the kit was a far cry from what I needed to fill that space so I thought that just getting bigger better speakers would do the trick.
Anyway, these focals are gone now, the holes are patched up and in their place, on Omnimount 60.0 brackets, are Paradigm Studio 20 bookshelf speakers, a cc-590 center on the mantle, and ADP-590 surrounds, which are actually coming in the mail today and I have not fully decided how to mount just yet. The ADP's however, will not be mounted on the wall behind the couch, on either side of the window like the focal's are now. They will most likely go on side walls, to the left and right of the couch. I was thinking of putting a couple of acoustic panels on either side of the window where the focals currently reside. The Studio 20's are pointed slighty in from an apporximate 30 degree angle and the cc-590 center as well as the Studio 20's are all pointed slightly down into the listening position. The center channel, as you can see, has to no choice but to be butted up against the stone, as there is just no other place to put it. It is rear ported and I've plugged the port with styrofoam and the sound seems to be quite good out of it. I can not hear any chuffing or boomy muddy bass/sound from it. Would it be of benefit to put some Roxul insulation behind it?
Also, I have replaced the 8" sub with the Premier Acoustics PA-150 15" subwoofer. I have an Onkyo tx-sr507 (which can be seen in the right side of the third picture) with Audyssey which I have learned is much better at setting up the speakers the way they should be than I am. So I've run Audyssey, it has the speakers crossing over at 70, etc., and I've set the subwoofer accordingly and have not touched the settings there after. The sub is sitting in between the big fluffy chair and the end table, basically under the receiver that is mounted to the wall behind the fluffy chair. It is a couple of feet away from the wall and pointed straight out into the room.
So here is the problem. With Audyssey set up, speakers set up to the best of my limited acoustic ability, when I put a movie in and watch it for a while, (LOTR, or Master and Commander, any good surround sound movie) it initially seems to sound awesome, but I still feel like I should be able to hear the voices clearer and as if that wasn't annoying enough, after a short bit, I notice that my ears are actually starting to hurt which makes no sense to me because I am not playing it louder than when I go into a movie theater and my ears aren't hurting when I'm done watching a movie in a theater. This led me to search google and I find a thing called "listening fatigue" and it seems to be from horrible acoustics more than anything. I know its not the Paradigms because I auditioned them for quite a while and bought them specifically because they were so much easier to listen to than the Klipsh's which I did noticed were hard on my ears.
So that is where I am at, and is why I am looking at acoustic panels, etc. I was thinking of putting a couple acoustic panels above the love seat at the first reflection, and maybe a couple more on the slanted ceiling above the couch at reflection points there, and was considering putting them higher up on the walls, above all the pictures to help deaden the sound echoing out of the cathedral ceiling. Also a couple on either side of the picture window. We have some nice thick black-out blinds that I can draw down in front of the window, as well as the curtains to help keep noise from bouncing off the glass. For a reference of scale on how large the room is, the tv is 65". Also, with the bookshelf speakers on the Omnimounts, they are only about 8" away from the wall so should I put an acoustic panel directly behind them as well?
Any insight into how to better this situation is greatly appreciated.
Thanks for all the great input so far!!
Edited by GrasaDeCastor - 10/30/12 at 9:13am