The water pump on my engine has two water ports, how do I determine which way the water will flow? I want to plumb the hoses so that the water flowing through the cutoff valve is in the proper direction going into the heater. Thanks

 

Well, let me see if I understand the question by offering this answer.

First most modern for water pumps pump out from the upper passenger side large opening to the top passenger side opening in the radiator. Then they pull in fluid from the lower driver side opening in the radiator to the large lower driver side opening in the water pump.

For heater flow, there should be an outlet nipple in your intake manifold that connects to the LOWER tube in the heater core - fluid flows throught the core - then out the upper tube in the core and back in via the long (anywhere from 3 to 8 inch) nipple sticking diagonally out of the water pump (from close to the center) toward the passenger side. Looking from the front of the engine toward the back it will point up to about 10 o'clock.

If you have a shut off valve, you want to plumb it between the nipple coming out of the intake manifold and the lower tube of the heater core which will prevent hot coolant from flowing out of the engine into the heater. The other port on the pump I believe, is on its very top and it is connected directly to the intake manifold with a short (3") piece of hose.

Am I close?

 

Looks like Julie has the jist of it. The small block Ford has two small hose nipples on the water pump, one for the bypass elbow that attaches to the thermostat neck on the front of the intake manifold, and the other for the heater hose coming FROM the heater. As noted, the hot water goes into the heater from the intake mainfold, and drawn back to the cooling system into the water pump. Julie makes an excellent point of having the hot water go into the bottom nipple of the heater core. It does work better that way.

 

One picture is worth 1000 words. Here's 2 pictures.

This a an FE engine but the set up for the two water pump openings you described should be the same. It's hard to see because it's chromed, but if you squint you can see the long nipple that accepts water in to the pump from the heater pointing up at about 10 o'clock (just above and parallel to the alternator bracket) and bypass already connected with the red hose (by the paper towel plugging up the dizzy opening) OBTW, in the second picture, the brass colored "inverted "L" thingy in front of the carburetor, is the intake manifold nipple where the coolant comes out of the engine and flows TO the heater: