@kickasskev day or night isn't the issue. The problem is nighttime is usually dark. Outside on a partially cloudy day at noon might not seem that bright since the sun isn't directly shining but your camera's exposure might show you're within a stop of full sun.

Pick an aperture and an iso that you can return to. In different lighting situation use the camera's built-in meter to tell you how long an exposure you're going to need to properly shoot a picture (don't worry about what you're pointing your camera at right now - just not something pure white or dark black - a nice mix of colors). The ratio of exposures is how much brighter or darker your light is. After you shoot a while you can set things pretty close by feel.

In broad daylight you might find you're shooting 1/1000 and at dusk you're down to 1/50 for the same ISO and aperture. Your autofocus has that much less light to work with (20x less) and you're going to show 20x more motion blur if you don't crank the ISO to balance.

I'm not sure cranking the iso of the main sensor has any bearing on the autofocus - I don't think it does. So in low light you're going to have trouble with the autofocus without the IR-beam or flash assist.