I'm not sure I understand the question entirely, but the fitting on the side of the water pump, and the fitting on the side of the thermostat housing base are the pressure and return line connections respectively.
If your question is will the heater warm up if you leave the by-pass in place, the answer is "some", but not much.
The bypass you describe is just a routine by-pass for a truck that doesn't have a heater. If you can snap a photo and email it to me, as the old saying goes a picture is worth a thousand words.
Sounds like you have a normal setup for no heater. The by-pass, in my opinion, would have zero effect on cooling because it is all under the thermostat itself. Whether you are by passing 6" or 6' through a heater core is immaterial to my thinking.
