Am I mistaken, or aren't both lines coming from the side of the water pump basically output lines? The return flow portion coming from the heater core is what goes down into the intake manifold where the ECT sensor threads in. If you go clamping a loop onto both of those water pump nipples, you're not going to get any flow because it doesn't have anywhere to go - it's all pressure and no return flow.
On mine, I have one nipple blocked off with a rubber heater hose plug clamped into place, and the other is that stupid little 90* elbow (y'know, the one that always eventually splits and causes headaches) that goes to the thermostat housing. So, I figure both of those lines are pressure lines, basically ... unless, of course, they're both return lines...?