I would like to ask a clarifying question here: are you saying that if an embedded SAM3X8E does not have the Arduino bootloader installed already, it is possible to program the chip with both the Arduino bootloader directly from the Arduino IDE?
I've been trying to research on how to load the bootloader onto the SAM3X8E and I'm not having good results- I have been using the AVR Dragon to load the bootloader onto ATmega328s for embedding, but it appears that the AVRdragon does not support the SAM3X8E. Any insight is much appreciated.