I always use pacifist, download the updates from apple website and extract it to the desktop with pacifist, run marvin and i edit the cpuid.txt file with the correct path, then i install the updates and run the marvin´s patch.

before edit the path


after edit the path


I update the kernel via terminal, first i rename the new kernel to mach_new and i copy to the root, repair the permissions, reboot and at boot type mach_new, if all is fine delete the older and rename the new to mach_kernel, that´s all.