I am running the vga as my primary monitor in FSX and the digital as the secondary monitor for gauges. However, the 780 is always going to see the digital as the #1 and the vga as #2. That's the way the 780 connections work and there doesn't seem to be a way to change it.
In one of the other threads RivaTuner and D3DOverride was brought up as a fix for VSync/tering in DX10 by Jeff Thomson.
In Jeff's explanation on how to use D3DOverrider, he stated Rather than threadjack the discussion, I'm starting another thread. ' These tweaks work fine with DX9, but DX10 seems to reject the cfg tweak or the Nvidia inspector tweak. Just set up the profile by clicking the plus sign and finding your FSX.exe file, and select 'Force VSync'. You'll either need to start D3DOverrider before you start FSX, or just have it run on startup so you don't need to. Since the option is already set, there's no fiddling with it.' I personally have mine pinned to the taskbar, so I just click on it whenever I need it. I'm asking Jeff if he can elaborate on the procedure.