I have lots of experience with converting skins to overlays to make them match maxis. If editing graphics within an existing package, you will need to ensure the pixel placement is precise, if not your new skin will not have the appearance you want. When the package is saved it overwrites the original. Usually, I will make a temporary directory in my MODS folder specifically for editing and I will copy the original mod to a safe location. This way I can easily revert back if not pleased with my modification.