In Figure 5 we can see the six heatpipes. Notice how the upper heatsink is actually made of three independent heatsinks (partially independent, as some fins are interconnected in order to make it a solid structure). Each set of two heatpipes is connected to one of these three heatsinks.
Scythe calls the system used on Kabuto M.A.P.S. (Multiple Pass-Through Airflow Structure). So, the air of the fan is directed to the motherboard, passing through the upper heatsinks and helping to cool the lower heatsink, as well as the components near the CPU, like the voltage regulator, chipset and memory modules.