Uh, yeah, what he said...
Pressure is tricky, and I have to really concentrate to explain it, because it was explained to me wrong the first time.
First, there's relative pressure (relative to atmosphere). Imagine that you have a tube, standing up, capped at the bottom, and full of water. There is some pressure inside the tube, from the water pressing down (thanks to gravity). That pressure is slightly higher than atmospheric. Now... at the water level itself (top), the difference between the pressure inside, and the pressure outside is zero: it's the same.
When you throw in a pump, everything goes awry: you create pressure where there might not be any, normally. If you can imagine a PC loop without a pump, you still have the relative pressures (relative to atmosphere), and the whole thing is predictable.
Add pump.
Now you've got an additional set of variables. If we stick to relative pressure (relative to atmosphere), the pump outlet will register the highest pressure point, and the pump inlet will register the lowest (in fact, the pump inlet pressure can be below atmospheric).
But none of that is a concern, for water cooling, except to note that if there's a leak in the loop, it'll either spill water, or suck in air, depending on where the leak is.
Obviously, the relative pressure drops, from the pump outlet, to the pump inlet, as the water goes through various components. It really doesn't matter in what order the components are, they'll all drop the same pressure.
The only thing that's different, is the relative pressure. The only effect it has, is on the joints. Example:
A heatercore drops 1 psi at a given flow rate. If the core is right after the pump, then those joints will have the highest pressure points, relative to atmosphere, but the core will still drop 1 psi.
If the core is at the pump inlet, then those joint will have the lowest pressure. If there's a leak there, it's even possible for the joint to suck air inside the core. (It's often the "invisible" leak that some people can't figure out).
The different relative pressure will have no measurable effect on performance: water is still a mostly incompressible liquid.