Aw, yeah you’re just misunderstanding how the custom layouts work. A “custom layout” is something you create one instance of; it’s meant to create those one or two special pages like your homepage. You only edit them in the Builder. That then replaces the content of whatever page you apply it to.
Have you checked out the videos series in your documentation on how the custom layouts work? It lays out it pretty clearly if it’s still not quite making sense.