I think it's a matter of your height more than anything, but I aim mine towards both, yeah the area of no window between the two is a little intrusive, but if you aim just at the lower window you won't see anything until it's right there.
Mine is aimed out the upper window entirely. I can't ever see anything out the lower window unless its right on my bumper. I'm 5'10 and usually have my seat upright while driving. I've noticed most people have theirs reclined back more...