The bootloader is preburned in ROM from Atmel and is called SAM-BA. There is no way to change it.
The desktop application that Atmel uses for uploading is called also SAM-BA, you can download it from the Atmel website, there is a version for Windows and Linux (no Mac). It works well, has a nice GUI, but its too big to include in Arduino distribution.
We used an open source alternative called 'bossac', written by Scott Shumate. This is a super-light tool, that supports a lot of SAM* cpu (from SAM3 to SAM9), that can be called by command line (like avrdude) and best of all, it runs on Linux, Windows and Mac.
http://www.shumatech.com/web/products/bossa(actually the site is down, i think its a temporary problem)
I did a lot of patches to Bossac in order to allow autoreset, and to do some workaround for os-specific problems during upload.
Scott Shumate helped a lot in this phase of development, he was very kind and responsive.
The Arduino patches can be found in the "arduino" branch of bossac github:
https://github.com/shumatech/BOSSA/tree/arduinohopefully these patch would be included in the upstream bossac in the coming weeks.