To install the custom firmware, once you downloaded Hakate and Atmosphere, extract the contents of both ZIP files to the root of your SD card.
For make the games work, also if you payed them, you need to install the signature patches. These patches allow you to run homebrew applications and games that are not signed by Nintendo.
For don't make Nintendo detect your custom firmware, you need to block their anti-piracy measures. This can be done by using the sysmodules and patches you downloaded earlier.
Learn more