The kernel contains a default root partition setting, determined at compile time (you can change it in the binary image with the `rdev` command). You can pass an argument on the kernel command line to override this default at boot time, e.g. `root=/dev/mmcblk9p42` to boot from MMC device 9 partition 42 instead of the default. The command line is passed to the kernel by the bootloader, so you need to change your bootloader configuration.
If there is an initrd or initramfs, it may override the root partition that was compiled in or passed by the bootloader.