I don't really get the backup feature? Since most things are saved to the SD card, what's the point of storing save data back to the SD card? I feel like I'm missing something here. Or maybe I'm just bitter that my SD card got corrupted a week ago and I had no backup on my computer =(
I think it makes it easier to backup just the saves, instead of having to copy over the whole thing. From what I see, they are stored in:
Nintendo 3DS/.../.../backup
Some details: Inside that directory, there are directories with names which correspond to the backup slot as a three digit hex number. Inside that is another folder, corresponding to a game's ID. For example, if you have a folder called 000400000006f800 (this corresponds to Wrecking Crew, EU) with a file 00000001.sav, this is an exact copy of the 00000001.sav file from the title/00040000/0006fb00/data directory. Considering this, using backups from one 3DS probably won't be possible on another system.
Still, it's also kind of handy that you can just make backups on the fly. If you're going to delete a save slot, you could quickly make a backup beforehand, if you might want to get it back later. This is especially handy, since you can have more than one backup per software, so you should be able to shuffle them around without switching the SD card around between PC and 3DS.
The one thing I'm not clear about yet though, is... How do you actually use the backups? Did anybody find the restore function?