Yes it is possible
You need to specify the rootfs location in Command line parameters passed to kernel. You can find the kernel compilation instructions in release notes: http://builds.96boards.org/releases/dragonboard410c/linaro/debian/latest/
Mention the rootfs location in following command found in release notes:
--cmdline "root=/dev/disk/by-partlabel/rootfs rw rootwait console=ttyMSM0,115200n8"
For instance, if RFS is placed in first partition of your SD card then:
--cmdline "root=/dev/mmcblk1p1 rw rootwait console=ttyMSM0,115200n8"
Then kernel will try to find root file system in the partition you've specified (mmcblk1p1) in the above example and boot using that.
Hope this helps!