I have struggled with this as well.
Originally I had two legacy Dynon units stacked and that worked fine for the capabilities that those units had.
With the 6,7 & 9 SBS models we have to compromise with the large screens available today.
My first go round with Garmin had a three screen setup with two screens (PFD1 & MFD) in front of the pilot and a third (PFD2) in front of the passenger. 95% of the time I kept the PFD2 on the full screen traffic monitor page. This worked out well for me.
When the Touch came along of course it replaced the PFD1 & MFD and since I did not have room for another large display I decided to eliminate the PFD2 and just put my 796 there in its place. The 796 can produce the same full screen traffic page that I was used to with my 3 screen setup and it can also get AHRS data from the GDL39 3D for a backup to the backup so to speak.
The touch really does a better job as a combined PFD/MFD than a two screen non Touch does separately. Hard to explain but if you have used both, you would understand what I am trying to say. The user interface on the Touch really adds to the usability of the setup.
Now Garmin is soon to ship the new 7" model of the Touch. This really helps me in that I can fit that screen in over on the passenger side without having to move the radio stack which I really really really don't want to do again. It will do a few things for me like bring screen redundancy back to my setup, bring a real PFD back to the passenger side, bring more screen space back to my system for use as a MFD so I can have more combinations of map, charts, plates, weather, traffic and EMS data up at one time. Granted it is still on the passenger side but in the narrow SBS cockpits like ours, it still remains quite usable.
On the other hand if you push the radio stack over on the passenger side far enough to make enough room for the two large Touch screens, it could really hamper usability for things that need a bunch of tweaking like audio panels, radios and GPS's. If you plan on having stuff that can be controlled from the screen, this is less of an issue. Also keep in mind that there are rules around where and how an TSO'd IFR GPS can be installed without needing an additional annunciator.
Like you if I were starting from scratch and even knowing what I know now about flying behind several configurations, I still would have to think long and hard about splitting up the two large displays. In my opinion the dual screen G3X Touch system is optimized when the PFD and MFD are mounted together side by side but on the other hand I am not sure I could stand my radio stack being that far over on the right side. This would be a non issue if I did not have a full IFR stack and had radios that the screens could fully control.
I would print out the different configurations full size and spend some time sitting behind the mock-up staring at things and thinking about how you plan to use the setup.