1. There is no way to run a minecraft server through a proxy because the minecraft client sends a ping to the server ip. If you ran the server through a proxy, you would have to give them your servers ip, rendering the proxy obsolite. If you want to run a minecraft server off your computer (I strongly advise you to invest in a dedicated server) and protect your ip, you would have to get someone (a friend, or the cheapest hosting plan out there) to host a server with jst about one plugin, lilly pad. Players would log onto that server (making it so they have no idea what YOUR ip is) and then possibly spawn IN a portal that takes them to your server.
2. If you are trying to directly connect to a server that is bungee corded to another server, you would have to connect directly to the hub server