SDA in surround

dongar, I've experimented with similar arrangements with my Home Theater. My Living Room is much smaller, so my results may or may not apply. I own a similar Pioneer AVR, although mine is a 72TX. My SDA 2ATLs brought it to it's knees very quickly, even with the receiver set for 6 ohm loads. The problem with all AVRs is the limited power supply. Your SRSs are running in 2 channel mode, therefore all power is available to them. I have no doubt your SRSs are using every ounce of the available power from that receiver. As soon as you add more speakers, that finite amount of reserve power must now be distributed between all the connected speakers, and runs out very quickly with multi-channel movie sound tracks. A separate power amp for the SRSs will solve that problem, and allow them to reach their full potential.
I used my CRS+s for surrounds in a 5.1 setup for over a year, and they worked beautifully, however others have not had success using SDAs as surrounds. They must be spaced properly, and setup just as you would if you were using them as fronts, no toe-in, parallel to the back wall. In my case, I mounted them on stands slightly above ear height. The area between them filled in nicely due to the SDA effect, and because of my side walls, the sound wrapped around you. Your room is much larger so I have no clue if your results will be similar.
SDAs do provide a solid phantom center channel, but it's only effective if you happen to be sitting in the sweet spot of the perfect triangle. If you have seating off to the sides like most home theater setups, people seated in those positions will not hear a strong center. I highly recommend a center speaker.
Your SRSs do go very deep, so a subwoofer is not required for 2 channel music reproduction. I turn mine off via the AVR when listening to 2 channel. Home Theater is a different beast however. The LFE or subwoofer channel is specifically designed for low frequency effects, and if blended into the SRSs, it will most likely detract from them. Separate subwoofers are really the best option, since they're designed for frequencies below 80 Hz for THX or 50 Hz which is what I have mine set for.
Regarding the AVR's auto calibration, the Pioneer does a fine job, and any calibration should be done with the IC cables disconnected.
I do find the resulting sound a bit thin however. My AVR can store 6 separate memory settings. I do the auto calibration on the 1st memory setting, and then do my own on the next one. Key information such as speaker compliment, distance and delay are carried over from the auto setup, so I manually set the gain for all channels with my trusty Rat Shack Digital SPL Meter. My own manual settings are the ones I listen to most, and rarely go back to the auto calibration setting.
Just my two cents.