I honestly cant figure this out. Im running a bungee based network. Ive tried using the normal LP.jar file and the bungee version and when i restart server, they will not create a folder for some reason?

You need to run the bungeecord version on your BungeeCord server and then restart it and the normal Bukkit / Spigot version on your Bukkit / Spigot server.

Also be sure to check for startup errors.