From looking at the schematic, you would remove the small 0-ohm jumper located at the "3.3" section of the "AREF" component, and move it to the "EXT" section.
You could then apply your new AvRef input to the AREF-pin on the PWMH header (the header with Pin13 and SDA1).
I like my schematic representation better than what's on the Arduino DUE page. I added a bit in the upper left to describe this (see PDF here):
http://arduino.cc/forum/index.php/topic,146574.0.html
-Chris