How does a microprocessor control its transistors?
There is nothing below transistor. The transistor IS the fundamental building block.

Transistors are used to form gates, and gates are used to build memory and logic, including the finite state machine that constitutes the CPU.

When the CPU runs, it fetches data from memory, and some of that data is actually instructions that tell the CPU what to do next.

If you really want to dig into this at the transistor level, you might find the following sites interesting:


Visual 6502 - a simulation of the transistors as laid out on the silicon chip.
Monster 6502 - a discrete transistor implementation of a 6502 on a large PCB.