Great question: we think that the stratification of Earth developed during the 50 to 100 Million year time period that the Earth accumulated.

How did the Earth "accumulate" ? It did so by a process geologists and astronomers call COLLISIONAL ACCRETION. That is two chunks of matter both in orbit around the nascent Sun collided ( in much the same way that even today meteorites fall to earth) and amalgamated. This processes happened billions and billions of times and gradually the Earth came to have its present mass.

As the earth started to cool, the layers began to form due to density differences. The densest (or heaviest) materials went to the center of the earth. You can think of it as the heaviest materials sinking to the center, and the lightest materials floating on top. That is how we got the layers of the earth.