You're certainly not the first person to be confused about how to patch the new devices.
You don't need KoboPatchFan; kobopatch is a CLI program. You just edit the YAML files to enable the patches you want and then run the appropriate script for your OS to apply the patches to a firmware ZIP file. kobopatch spits out a KoboRoot.tgz file that you copy to your device to do a firmware "update" with the patches.