If the SAM3x does not have any software in it you cannot connect it through USB. The Arduino Due has a bootloader in it that handles USB and writes new programs into memory and starts them.
Guys, there is NO NEED FOR A BOOTLOADER if you are using the native port, i can even upload using the arduino IDE. Though you have to erase the code with a push button to upload a new one.
Actually it does, but it is build in. I missed that one when looking at the datasheet. Learned something new. Thanks for the feedback. Good luck with your project.