Run setup.sh or setup.bat depending on your operating system. This will ensure you have the mods installed for your instance.
You will also need Twitch Export Builder. You can install it from that link or go get github.com/Gaz492/twitch-export-builder.
The .build.json identifies what files and folders are to be overrides for the modpack.
The .gitignore is pretty strict and only includes files that should be overwritten since all mods create their own default configuration. No point in checking them in if they are generated on instance run.
If the override should override user configurations on modpack update, then modifying the file in the ./config/ directory is where you want to do this. This is usually not a great experience but some cases this is needed.
If the override is for default settings for the mod pack for a better experience, the ./defaultconfigs folder is where you should look. Add a file with the same name as the file you want to override with a default value. It is best to only include the keys you are overwritting in here.
If you are changing recipies or kubejs is installed and looks in the kubejs directory. https://kubejs.latvian.dev/ more information can be found here.