Being able to at least select which output is the primary would be cool.
Until then, this is hard coded in your video card BIOS.
My primary display is connected to the Display Port, but my 660 GTX insists that the DVI port should be the primary output. So when I connect a secondary display to the DVI port all activity is on that display until Windows or OS X is done booting.
GraphicsEnabler does support two GPUs but for the time being I believe it only works if they are from two different manufacturers, ie you can have Intel on die HD4000 working along with an Nvidia or ATI GPU.