As mousemonkey pointed out there is the option to turn it on or off in the software. But the question is why bother? It's not like its going to save anything. Both cards would still be powered and its not going to really make any difference in running other software.
Yeah, I agree with both above. Why disable it unless there is an issue or you want to run multiple monitors? Besides enabling/disabling SLI in the global settings, you can even choose to automatically run each game using both cards or one card. if there is not game profile for an odd game, you can create one yourself.