How to do it?

In the picture, a layer of stone, other stone and shale.

First, this is not three layers of stone. There is stone and deepslate, which are each two separate biomes in most cases. The shale is most likely a feature. However, in general, you can either create three biomes each with differing depths so that they may be stacked on one another or you can use features to replace blocks within a certain area based on certain rules.