I've never set water cooling up before. However, from my research and from a bit of guesswork. I'd say you would be better of doing two loops. For example, instead of putting a 360 and a 240 on one loop. Use a 360 and a 240, with two loops. That will separate the components, so that your gpu(s) will not cause your cpu's temps to be higher than needed, and vice-versa. If you're going to have high end gpus (GTX 580, radeon hd 6850+, etc) then i would go with a dual loop. Personally i think gpus get hotter than cpus, so i would put the 240 on the cpu and the 360 on the gpu(s). But as i said i've never done water cooling so i may be wrong on that. I'm willing to bet a dual loop will beat a dual rad, single loop, every time.
Right now I'm running 2 6950 2gb overclocked to 900/1375 and a 2600k overclocked to 4.3ghz, and the temperature of the 6950s are minimal difference, and the CPU never goes over 50c even though it's third in line for cool water after the 2 GPUs and the pump.