The standard way to handle the hwclock on linux systems is to save the system time to the hardware clock during reboot, and restore it on boot. This is done through init scripts.
So in buildroot, you would add an init script that ends up in /etc/init.d/Sxxhwclock, typically using a rootfs overlay, or alternatively with a completely custom target skeleton.
See http://buildroot.uclibc.org/downloads/manual/manual.html#rootfs-custom for more info on customizing the target rootfs.