the manifold gets blocked off to prevent the hot water returning to the radiator from returning through the water pump and mixing with cool return water. Think about the flow. Coolant flows from the front of the block back. Returns from the head to the water pump. The water from the head is hot  and connects to the water pump next to lower radiator hose, which is cool water from radiator. By putting heater core\head return line into the manifold it takes away heated water from mixing with the cool water.  The bypass from the front of the manifold is for the same reason.
 I run Edelbrock heads and have both heads plumbed for return lines. Don't stock heads have the port on the drivers side head just blocked? If so, just tap in a nipple like the other side. It's been so long since I looked at a stock head I forgot what they look like.  

I run 6X heads. Returns are pressed in and BIG 1.1875". Found a co in California that sells them. Just need the Tee and restrictor washer and I'll be good to go. I'll let you know what I run once it's done. Thanks......Joe  

If the carb is set too lean it will heat the engine up. I also like to run the distributor on a ported source, so not to add a lot of timing at idle.