We're talking about idling now, and yes, sequential would ideally be the way to go in order to be most efficient and less emissions. But at higher rpms, the injectors are open longer than the valves anyway so it makes much less difference.
I agree messing with the injector open time setting, alternating and 2 squirts will net you a bit, but if the injector is large enough, you'd be better off with simultaneous - as long as you have the fuel pump necessary to keep the pressure up!