The whole idea around jumping the PSU is so you can turn on the PSU and anything attached without involving the motherboard.
Namely, if you are filling up the loop and using the pump to push water through it, you are not providing any cooling to the CPU or other parts in the loop. So if you turn on the rig normally, your CPU/whatever will burn out since they aren't being cooled. By jumping the PSU (and disconnecting all power to the mobo and GPU) you can turn on the pump without supplying power to the mobo.
The green is the "on" signal for the PSU, the black is just a grounding wire. Connecting them makes a circuit and the PSU turns on.
Their are dedicated tools for jumping the PSU like this.
http://www.frozencpu.com/products/3223/psu-173/FrozenCPU_20-pin_Power_Supply_Jump_Start_Connector.html?tl=g11c133s88
Or you can just use a paperclip and just use a diagram of the 24pin connector too know which connections to use.
This guy did it wrong and turned on the PSU normally through the motherboard with everything hooked up.
http://www.youtube.com/watch?v=2LjqCoVbZ_g
At about 1:19 you can see the board flashing to indicate that the CPU is overheating.
The reason why he managed to kill the pump (and likely the rig) was because he sealed the loop when filling it, the air has no place to go so it stays there and stop the flow completely. You dont seal the loop until the water is flowing smoothly.