I can honestly suggest that you will want to remove your motherboard and use a real mount on the cooler... There are some coolers that will allow you to mount without the removal of the motherboard, but in my experience they suck.
Some things to keep in mind when building your loop here are
1. Pick a tubing size. (1/2" 3/8" or smaller *gasp* if you are going to use aqua computer gear).
2. Figure out how many total blocks you will need. (Important for picking a pump)
2a. Are you planning on cooling the North Bridge, Mosfet. Video card, etc.
(On your board, it will be rather expensive to watercool the NB and mosfets)
3. Where are you going to mount the rad (internal, external)
4. Calculate your current wattage to pick the right size rad. If you are going to do Overclocking (and overvolting) you will need to add that in to the number..
5. Once you have a general idea of the above you can start making decisions on fans, this is a *very* important part of watercooling that most people dont consider. You want a fan that produces a pretty high static pressure through the radiator to pull the most heat. Another thing to keep in mind, without fan spacers you are loosing about 15% of your total cooling surface of the radiator due to to your fan motors being directly mounted to the rad. The fan spacers will fix this, but at the cost of space.
6. I noticed you mentioned Putting the pump in the open area under your psu.. Some die hards will rant endlessly that you want your pump and the lowest point in your loop for minimal wear and tear since gravity is constantly feeding water to the pumps inlet. I do not use this configuration, but I would certainly reccomend it to others. Once you figure out where you are putting your Rad it will be much easier to advise on location of a pump.
In case your wondering, here's a shot of my rig.
I have 2 rads, 1 3x120 Swiftech QP series and an older (and exteremely loud) Danger Den 1x120 rad out back. I run a pre D-5 Swiftech pump.
Since I built this so long ago (x2 3800+ *939*) the rest of my parts are extremely dated.
Edited by EverestX, 02 June 2009 - 11:08 PM.