Hello Aditya Nagal,
The ROM code allows to enter a Serial Download Mode which can be used to flash images to the boot device (SD card, eMMC, etc). You may find more details on how this works in section 8.2.4 of the i.MX6Q Reference Manual (link below)
http://www.nxp.com/assets/documents/data/en/reference-manuals/IMX6DQRM.pdf
You may use the Manufacturing Tool to download images to your board this way. There are already profiles for the i.MX6 SABRE boards but you may customize the Manufacturing Tool for your own board. There are Manufacturing Tools for the Linux and Android BSPs. You may find them under Programmers on the Software and Tools tab of the Boards page. Please look at the documentation provided alongside the Manufacturing Tool for more details on how the profiles are programmed.
I hope this helps!
Regards,