I apply palm mute with the fleshy edge of my palm, ( the side nearest to the pinky). I place my hand on the bridge, closer to the tailpiece than the pickups. By rolling my hand a little bit, I can control the amount of muting I apply to the string(s). The best part of this technique is that your hand is 'anchored' at the bridge, so you always know exactly where the strings are. You may have to shift the placement of your hand once in a while to accomodate the reach of your pick, but I find this method works for me.