Are you trying to do 2-screen surround or a 1+1 configuration?
I use a 1+1 with one GTX 680 hooked up to two monitors: one 1440p 60Hz monitor (for MMO games and daily usage) and one 1080p 144Hz monitor (for FPS games). To change back and forth, I just go into the NVIDIA Control Panel and switch the "primary display" depending on which monitor I want to game on, and the other monitor becomes my secondary screen. No issues with the fact that the two monitors are different refresh rates (or even different resolutions). I don't think SLI would make this any different.