The more places you can mist the roots the better, but as long as they are getting nice and wet during the pump on times, that's what's important. If I had to choose one place, I would mist on the side of the roots. The bottom is going to end up getting wet no matter what you do. The point of a mist though is that it kind of floats around in the air and covers everything, so where you put the nozzles shouldn't matter a whole bunch, unless you are spraying more than misting. Only misting is aeroponics.