First drop HackedServer.jar and HackedCore.jar to your /plugins/ folder and restart your server.
If all goes well you should get something like this :
Start by installing HackedServer on every spigot servers as explained previously. Be sure that
bungeecord is set to true in your spigot.yml configurations and
ip_forward enabled in your bungeecord config.yml.
Then drop HackedServer.jar (it's the same jar as for spigot) to your bungeecord /plugins/ folder and restart it. There should be only a simple log saying that the plugin is well loaded since its main feature is fixing bungee incompatibility (it also brings some debug features):