For all with the same problem here is how I solved it.
onready var server_tree = SceneTree.new()
# add your server scene (it needs to have the same name as the singelton which handles the client connection)
To start the server call InitServer.start_server()
Inside of your Server.tscn you can start a server via the standart
get_tree().network_peer = peer
For rpc to work you have to know that the script which calls the rpc has a path. In your server scene you must have your script which handles the rpc under the same path.
So if you autoload your client manager as Networking its path is "root/Networking". Your Server.tscn is added to the root. If you name the root node of the scene its path is "root/Networking" as well. So rpc should work.
Tell me if I misunderstood the stuff with the paths but it works for me.
Note: I havent tested all details of this.