The default boot environment is built to run form the first partition of an ext4 formated SD card. It is seen as mmcblk1p1 from the target.
this operation is risky for your development host: you can simply crash your system. Please pay attention while running these actions.
format the SD card as an ext4 volume
mount the SD card on your host
as superuser, extract the rootfs archive on the SD card:
# cd <SD card mount point>
# sudo tar xvaf atmel-xplained-demo-image-sama5d2-xplained.tar.gz