Make arduino due by myself?

Hi all, now, i have a project that need to use the the atsam3x8e mcu, i can working with the arduino due but with a new atsam3x8e i have some problem with it: 1/ where can i find the bootloader for it because i want to programming the chip by the usb connection, i only find the bootloader for the atmega16u2 in this path C:\Program Files (x86)\Arduino\hardware\arduino\sam\firmwares\atmega16u2 2/ can i connect a segger jlink with it to program ?

I don’t think it has a boot loader in the same sense as the other boards.
http://playground.arduino.cc/Bootloader/DueBootloaderExplained

thank you very much, very poor for me !! and can you suggest that how can i can programming for atsam3x8e ?. use the j-link is ok, or how can i get this bootloader

The Arduino software uses a tool called bossa (or bossac?) to talk to the SAM3X hardwired bootloader