That guide is terribly confusing and I think certain details may be inaccurate though, primarily in how they describe the front and back of the pump. I would think when they say 'front', they mean the part facing the water source and the back would be the output. The back of the pump in fact is impassable to both dwarves and water, while the front is passable by dwarves and probably water, going by my definition that just seems to make more immediate sense, to me.
I found their choice of front/back highly counterintuitive, but once I figured that out the rest basically makes sense. The arrows on the diagrams show the flow of the water through the pumps, meaning if the arrow is pointing to the left the pump is actually drawing from the right. I think this might be why they describe the 'front' of the pump as actually being the impassable part that blocks water and pumps out water to the square next to it.
In the first, most-graphical diagram, the part with a wall that holds back the water is the dim X that you see while placing the pump, just like workshops, blocks movement (and also water in this case). The part with the gear on its side and the wooden bits is the bright green X you see when you're placing the pump. This is where a dwarf stands to manually operate the pump, just like with workshops the bright area shows where dwarves can move and probably water will flow through this square too if you let it. Naturally a dwarf can't stand where he can't walk, and when he's operating the pump he'll be standing right next to the water-source, meaning the square you can walk in will be placed right next to the water.
Sorry about explaining it over and over like that, but I had a really headache-wracking time trying to figure out how to orient pumps, and so I don't want anyone else to struggle like I did.