I have a question: can you please point to the .bin file that needs to be uploaded to the SAM chip?
Also, I think in your post above you posted an incorrect link by mistake, referring to using Arduino's bossac tool.
I am also making my own Due and am a little stuck on this step. Thank you!
There is no bin file that needs to be uploaded.. The Sam-chip will come preloaded with a bootloader.. So it will work out of the box! The link isn't a mistake.. Let me try to explain it in simpler terms:
- In case of uploading (a sketch) to an ordinary AVR (for example the atmega328/UNO) then you'll upload a HEX file with avrdude..
- In case of uploading (a sketch) to a SAM-chip (for example the SAM3X8E/DUE) then you'll upload a BIN file with either BOSSAC or SAM-BA...
- For a newbie I recommend sticking with BOSSAC for uploading because it's simpler.. SAM-BA has a GUI but there is a lot of boxes and settings (a newbie will simply get confused and run back to the arduino forum for help =P)..
If my explanation isn't clear enough then let me know exactly what you're stuck on and I'll do my best to help you!