I found some information on this question elsewhere in the forums (-a), but not really a definitive answer.

I am installing a Scythe Infinity cooler/heatsink on my MSI Socket AM2 MB and CPU. The fully assembled unit will project horizontally from the mount, and the pipes will also be almost horizontal. Will the unit function properly in this orientation?

You mean the pc is a tower? Why not? If you're talking about the fan orientation, it should be blowing onto the rear fan.

As AK said - It'll be fine. Just check that the CPU cooler's fans exhaust towards the back of the case and your exhaust fan so the heat can be drawn out efficiently.

They have capilary action so the fluid will always rise to the top of the cooler when hot.

they are right, fans blowing towards rear