Submerge both the main and emergency in the sump 1" below the water line. If you gonmore than that the siphon may not start.
In the overflow box tou can run the main drain without a stand pipe as long as the sump can handle the full volume of the overflow + whatever drains from dt when pump is off. If not youll want a stand pipe a minimum of 6" below the max water level in the over flow.
For silent operation the emergency drain should be around 1/2" below the weir.
Adjust the gate valve on the main drain closed a little until the water level in the overflow is even with or just trickling into the emergency.
Setup like this it will run silent and if the main ever plugs the emergency can take on the excess. Also if main is plugged completly, the emergency has a chance to go full siphon as long as the sump end is submerged.
For more info...
http://gmacreef.com/herbie-overflow-reef-tank-plumbing-method-basics/
It can seem confusing but it's very simple. The hardest part is cutting the standpipes to the right height. I would make thr pipes longer than needed and cut them shorter and test until it's working the way you want it.
HTH
Jim