You can use the .bin file generated by AS6 located at:
Then load your .bin file to Arduino Due using bossac.exe that comes with
the Arduino IDE (...\arduino-1.5.6-r2-windows\arduino-1.5.6-r2\hardware\tools) as follows (cmd command line):
bossac.exe --port=COM12 -U false -e -w -v -b yourfile.bin -R
Notice that I am using port 12 because that is the port in my laptop where my Due is connected.
Remember to press the delete and reset buttons of Arduino Due before run the bossac.