You can go to eshop and get the updates for your games. Or you can get the update.cia file from that site. But if you go eshop version remember that the updates on eshop will only work for your region cia games. For instance, I had the super smash EUR cia installed and when updating in eshop the game still asked me to update. It took me 2 days to figure out why and then I realized I was using a non-USA cia file of the game.
