The original 254 cyld. casting was designed for a rear exh. engine. It was soon used for the side exh. eng. as well. The extra water ports are there as an option for the builder to plumb as he sees fit. You always want the cold water going into the motor low, and the heated water to exit high, in order to purge out as much trapped air as possible. Also, the hottest part of the cyld. is at the exh. port. If you can, it's better to send the water IN as near the exh. as you can. In fact for more northern climates, it can help to put the water through the exh. cooling flange first, then in to the motor near the exh. port. One line in, and one out, should work fine for that motor.