I'm not sure exactly what you're asking. The chip's inputs and outputs are wired from the chip's pins to metal pads on the die. These signals then routed (mostly) through various metal layers to the transistors. For a MOSFET, the source and drain are in the silicon, while the gate is a polysilicon layer over top. The source, gate, and drain usually have contacts connecting them to the metal layer.
I wrote a post explaining how some of the MOSFETs in the Z-80 microprocessor are wired up. It might help you: http://www.righto.com/2013/09/understanding-z-80-processor-o...