If you somehow find the update in .XCI format, which I highly doubt, then its not just a game update; it would have to be the game plus the update. Updates can't be in .XCI format because it doesn't make sense. .XCI files are games you mount. You cannot mount an update.
Assuming you do find the update in .NSP format one way or another, it doesn't matter where it goes but obviously, if it is installed to the SD card, the update will only be applied when that SD card is inserted. And if you are installing the update rather than grabbing it from online, it will only work in CFW.