If you are in Windows, you can use my modded ide:
http://arduino.cc/forum/index.php/topic,118440.0.html
It includes 'autoclear' in the monitor (if more than 1 second elapsed since last data) so you can add a "delay(1000);" in the moment you want to print a new screen for your outputs and keep them tidy and not lose any second (or 10 hours).