you cant cool the motherboard w/ watercooling, just anythign they seel a water block for and i believe the power comes from the PSU. And you use water blocks made specificaly for the part your trying to cool (video, cpu, chipset, HD).
1337 n00beh, will this be the first water cooling saetup you have had? If it is, I advise against building your own. You should get a kit for your first one, and then when you know what you are doing build your own. A good starter one is the Thermaltake Aquarius 3. Dangerden also has kits, give one of them a go. But if this is your first water cooling system, I wouldnt advise you to build it yourself.
Also, you can get pumps that plug either into your mother board via a fan controller, directly to the psu via a molex connector, or you can get one to plug straight into your hosue outlet.
I disagree, I built my own from Dangerden and a bit of modding, there's no difference between a prepackaged kit and buying the parts seperately, you still have to set both of them up in the same fashion.