ATSAM3X8E on breadboard Bootloader

Hi,

I am trying to create my own Arduino due board, I mean realizing the board in my project but I can't seem to fund the bootloader and how that can be installed into the ATSAM3X.

Please help.

No need to install, as SAM-BA bootloader is already factory prestored there:

http://forum.arduino.cc/index.php?topic=234973.0

Will I then need to include the ATMEGA16U2? If so what about the code on that?

How can I program the 16U2?

Please try to read the referenced link in the other post. There is also the link to the source code in the 1.5.x development branch for Dues.