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Well I somewhat understand most of it, and it only gets more crazy.

I mean, it only really works because there are so many layers to it.
You get the basic circuits, then you get them together and make a way to tell them what to do.
Then you make it easier on yourself by making a language that then talks on your behalf to the parts.
Then you make a language that talks to the language that talks to the parts.
And then you make another language that talks to the language that talks to the language that talks to the parts.

(For reference: python gets translated to C++, and that gets translated to assembly, and that talks to the CPU)