When you switch to a game (pokemon x/y or/as for example) it will check for updates on the game and a scrolling txt on the bottom of the top screen will say something about an update for the game, when you press "A" you get the option to play the game or to update it (Button "Y") just update the game, like you should do on a real cartridge, voila game updated, next time you will not see the scrolling txt about an update