Saves are in two forms, EEPROM and NAND.
EEPROM is stored in a special area at the beginning of the SD CARD
(make sure to move to another game (blue button) if you wish to backup a save using the DiskTool)
NAND saves are stored inside the game data area just like a real game
(you don't need to move to another game before backing up NAND data)
I Hope that helps.