Inside the ROM file itself. (I guess it's not really ROM then, is it?Where do card2 saves go if not on the internal SD?
Both can back up saves. I prefer .3DS though, because you can just batch copy a whole bunch of .SAV files instead of clicking 'Save Data Backup' for however many .CIA games you have.So.....if Imma ignoring 'em and only wish to back up my saves, then what would be good?