I'm not entirely sure why you even need to bother with the AMD's and nVidia's config software. Both Win7 and 8 natively support three monitor setups, and with monitors of different resolution/size.
I'm at work in my cubicle and I'm currently writing this on a basic HP Probook 6575b which uses the AMD A6-4400M APU (Radeon HD7520G video chipset) connected to HP's docking station. I have (2) Samsung B2230's side by side and an HP P221 hanging on the wall in a portrait orientation.
Using basic Windows configuration, I have the P221 monitor offset so bottom portion is about 2" above the bottom of the Samsungs, and extends about 10" above. Even though the physical screen of the P221 does not align with the Samsungs, when I drag windows across the monitors, they stay exactly lined up; they don't get that disconnected offset. (I realize it may be hard to visualize).
The point being is that Windows' native monitor resolution settings will allow you do the basics needed to configure your three monitor setup as well as set things like offset and orientation. I think what throws off most people is that they don't realize that in the screen resolution settings, you can drag your monitors around and reorder and align them as needed.
One other tip... rather than have your monitors bezels next to each other, find your normal seating position. Now take your outer monitor and move the bezel so it's directly behind the middle monitor's bezel. Effectively you should be able to achieve the visual perception of only a single bezel divide instead of a double-wide.