Once you have rebuilt the kernel and the device tree with SPI enabled, you can install the new kernel from a SD Card without changing your root file system. Copy your new kernel image onto a SDCard and plug the SDcard into the system you want to upgrade. Run the following commands:
sudo dd if=boot-db410c.img of=/dev/mmcblk0p8
sudo reboot now
The system will reboot running the new kernel. Of course I would recommend testing everything on a test system before upgrading your running production systems.