it gives 3 folder options/ methods within that desktop folder for you to choose from.
one is a patched apple HDA file that you can replaces the one in S/L/E with directly.
second is a dummy HDA if you do not want to replace AppleHDA in S/L/E
and the third are clover config patches you can apply to your clover config. but i think that might need DSDT patches for HDEF.
each has it's benefits but results should be the same if used properly, from either of the 3 methods. just choose one do not mix.