When in TwinView the system makes my Primary Display my BenQ 24" and my Samsung 32" TV the second screen, Great!
Trouble is: When I make a basic xorg.conf using NVIDIA-SETTINGS I reboot and it gets them backwards, the image that Ubuntu thinks is the BenQ primary (according to what All Settings > Displays & NVIDIA-SETTINGS both say) is actually showing on the TV, and the BenQ is showing a big grey screen, but the cursor works.
One final complication is that my TV runs through my AMP in order to get digital sound, it shows in Ubuntu as 'Onkyo blah..'. My Monitor is using the DisplayPort of my GeForce GTX 670 while the TV is on HDMI, this may be what's making the TV primary (as it carries the sound).
If I make another conf which disables the TV it reverts back to TwinView on reboot, here's the conf for that if its worth while: