HardwareSecrets tested several ways to apply thermal compound on a CPU in order to find out what is the method that brings the best performance. Check it out over here. The conclusion is that putting a small drop of themal compound at the center of the processor is the best way to apply thermal compound.
"If there is one thing about computer hardware where there is no consensus, it's the right way to apply thermal compound on a CPU. Today, we present seven ways to apply it, showing how the CPU looks after removing the cooler and how each way affects cooling performance."