Hello pracas. That is in my pending list to-do. I got my Atmel SAM-ICE JTAG emulator/programmer last week but still having issues to connect it with Due. It's a matter of time for me but I am a kind of busy with my work and other projects. Please, keep an eye of my post:
So far for my understanding, using a JTAG is the only way to program Due through AS6. You can do it with Arduino UNO without problems thanks to avrdude.exe, but the SAM3X8E is another story. regards!