If I am understanding correctly, there are three drains (two with gate valves and the emergency) ? If so, only one should be dialed into a full siphon(main). The second one should have the valve all the way open. Your main drain should handle the majority of the water with the overflow slowly filling to the secondary drain (which should sit higher in the overflow than the main drain), which should handle the small amount that your main isn't. The emergency drain should sit just higher than your secondary stay dry unless there's a clog in one of the other drains preventing the first two handling the incoming water.
Depending on how deep your overflow box is, it helps if the secondary sits at a height just below the top of the box (just under the teeth of the overflow). If your pipes are sitting too low in the overflow, this will cause a bunch of noise you probably won't be able to silence. Outside of dialing in the gate valve of the main drain, the height of the stand pipes are key.
