Typically, the water jacket on an intake manifold is used to heat the manifold. They run a lot better that way in cold weather, and prior to the engine reaching normal operating temperature. I'd recommend hooking it up. My '49 Dodge ran very poorly when cold, and took a very long warm-up period before it would run well until I connected the water jacket to the heater hose outputs on my cylinder head.
Tuning multiple carbs can very tricky, why add the complexity of dual carbs into the mix? Since you're working with a completely unknown setup, you will have to figure everything out for yourself as it is.
