Hey,
So if you've ever tried swapping a Hoenn ROM (Ruby / Sapphire / Emerald) into the Pokémon Leaf Green NSP via LayeredFS, you probably already know the pain: the game runs fine, "Save complete!" message and everything, then you reboot and… no...
on the root of the sd you should have a "tico" folder, inside that folder the cores go in a folder called "cores".
example folder structure should be
/tico/cores/tico-dolphin.nro