Easiest way to update... (this only works if the app is the same region as your 3ds. Out of region games and some eShop games need an update in CIA form)
- turn on your wifi
- highlight the game / app on your home menu
- it will say "an update is available for this title bla bla bla"
- launch the game / app and a menu will pop up saying press Y to update and A to launch the software.
- press Y
- wait
As Posghetti said you can update form the eShop, but I wouldn't suggest it. There's no need to use it and in specific cases the eShop can actually delete some of your installs. This way updates from the exact same servers, but doesn't require you to launch the eShop. You can also find most game updates in CIA form on "that ISO site" if you want to update manually or if you need to update an out of region game.