Your pump is WAY overkill for the rest of the setup as is. I would suggest going for a WW or a Cascade if you can get it. You also have plenty of capacity to cool anything else in your system that gets warm.
In nearly any cooling setup the biggest barrier on improving the cooling is the transfer of heat from the rad to the air. You will transfer the most heat by sucking ambient (room temp) air through the rad, as opposed to putting air through the rad that has already been somewhat warmed by going through the PC case. This would suggest that putting the rad in the top of the case is not the best approach (also this will tend to make the rad catch air)
Dual rads in your setup is again overkill, but since you have them, I would say you might as well use them. I would probably make a custom box out of wood or MDF with the two rads at the front, plumbed in parallel, the pump and the res in the center of the box near the bottom, and the fans near the back blowing out. Seal the box except for the fans and the rads so that the box acts like a giant shroud. From the box run two tubes w/ quick disconnects to the system box which would only have the blocks and their plumbing in it. Seal the system box except for the lower front and the PSU which should provide enough airflow to cool the rest of the system.
As to plumbing the blocks, I'd put them all in series given your pumps capacity and the blocks you are using. If you went to a multi outlet block like a WW or Cascade, I would consider running everything into the CPU and then splitting the flow through the lesser blocks, using the CPU block as a splitter in effect.
I would avoid the bay type res, I've seen lots of reports of them leaking, and that they are a pain to fill. If you go with the custom rad box like I suggested, you'd have lots of room to be creative. I would probably go with something custom built out of fat PVC that hooked directly to the pump inlet, but there are lots of options.
Gooserider
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Designing system, will have Tyan S2468UGN Dual Athlon MOBO, SCSI HDDS, other goodies. Will run LINUX only. Want to have silent running, minimal fans, and water cooled. Probably not OC'c
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