The remaining 1% is the 2nd SVS PB12-NSD? That's actually a pretty good idea. A 2nd 12" sub will give you a flatter (or tighter) response, while a single 13" sub will give you a slightly deeper bass. Between the 2 options, I'd choose the flatter response.
You need to locate them equidistant from your main listening position, which means that you'll probably just put the 2nd one to the right of the center speaker.
Make sure that they have the same volume level at the rear. Set phase to 0 for both. Disable the Low Pass Filter at the rear of the sub. Run Audyssey again for just a single measuring point. If the Sub trim is -12 db, lower the volume of the subs even more until the sub trim recommended by Audyssey is at most -10 db.
After that, you can experiment by moving the subs closer to the corner and see what you prefer.
I also suggest you try to put your 2 front speakers a bit away from the side wall and a bit more forward. I think the frequency response will also become flatter. Same with the center channel - you can move it slightly forward and make sure that the tweeter is pointed at your ears when you are at the main listening position, else, lagyan mo ng kalso ang stand. Experiment ka lang. Even small changes (8" to a foot) can make a big difference.
Good luck!