Loop order makes very little difference. Unless you have (very) low flow, the water only warms up by a degree or two as it passes through a block thanks to water's high heat capacity, so the difference in your CPU or GPU temps should be less than a degree.
It makes more sense to plumb your loop in a way that's short easy to manage. The obvious exception is that reservoir should come before pump because it makes filling and bleeding so much easier.
Pump/Res-> Top Rad, ->Apogee-> 5870-> 5870-> Bottom Rad-> Pump Res. You could of course reverse it so the bottom rad is first, but you will not get much if any differance other then maybe how long it takes to bleed.
Either way would give you the shortest amount of tubing.
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