Tracking a window under another window without adding one windows effect when they cross??

Is there a way to auto track a window and have it pass over another auto tracked window without the effect that is in say the bottom layer showing. Another scenario.....you are auto tacking a man in a shot that runs behind another man but the man that is behind has a window with some pretty heavy correction but at the moment he passes behind another man you want the effect to seamlessly pass under the guy in front? Can this be done without the old "Second Pass"?