Well, I don't remember it clearly, but you can backup CIA content and card contents.
It is two different options.
And when you backup a save, generally it backups all content together.
You can even backup savedata from a game card and restore it to a CIA version of the game.
In order for you to restore your save data (in case the system collapsed) you must first install the game.
What else...
Oh, if your sytem breaks and you have to reformat you will have a different structure for the Nintendo 3DS folder, so copying that folder will not be a good backup of your saves.
But with savedatafiler that does not matter.
You must backup the file that corresponds to your game.
Look for the game ID in the CIA, it matches the ID for the save file you must backup.
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You can find the ID for the game when you are installing the CIA, or looking at the installed CIAS.
The ID is just there for you to look in the install menu of BBB.