Great, thank you @cmaglie and @Graynomad.
So the conclusions are:
(1) Atmel has pre-burned bootloader into ROM for all SAM3X8E ic's as sold, so no such thing as "Arduino bootloader" any more as was the case for previous Arduino boards.
(2) USB/Serial uploading of "sketches"/firmware (or the corresponding hex files to be specific) can be done via SAM-BA software, or via Arduino 1.5 IDE (which uses bossac tool by Scott Shumate)
(3) And as @pyro_65 states, firmware uploads may also potentially be done from a mass-storage device via the USB host (?).