Network Instantiate problems

I am currently trying to write a small server and client for a game I am making with a small group. I am still quite at the beginning, just creating and testing the login/register system, with some basic game logic running on the server.

I want to create a completely authoritative server, the clients handle input and output only. I want to have the game world running on the server, and when a player connects, he gets thrown into the 'persistent' world.

I am currently struggling to make the 'persistent' thing work. I am using Network.Instantiate(), and it kinda works. I suspend working through the queue of buffered objects until the correct level is loaded, but I have the feeling this is not the best way of creating a persistent world, so any suggestions are appreciated.

The real issue I am having is even more problematic: the instantiated objects don't appear on clients, when I use a standalone build, only in the editor, and I don't have any idea what's causing this.