Updating games with "(embedded update)" cias?

I assume that the embedded update has the whole game in the cia file ex: "Crashmo (USA) (v1024) (Embedded Update).cia". If I already have the older version installed and I want to update with this embedded update version do I need to un-install the old version first, then install the new one or can I just install the embedded update version over the old one? I want to know because it will be a hassle to uninstall everything first, then install the updated games. I would try it but I am afraid I might corrupt something by installing the same game that is already installed. I doubt Nintendo does it this way so not sure what would happen if I did it like that.