You start by reading hardware documentation and you don't need to understand the machine at an electronic level. It's not a simulation of digital circuits. It doesn't need to be that complicated. An 8-bit CPU is a simple state machine with only a few bytes of state (registers). You can read the program one byte at a time and simulate whatever operation the CPU would do after reading that byte. They are very simple operations like adding and subtracting numbers, loading and storing bytes.
http://www.6502.org/users/obelisk/6502/registers.html
http://www.6502.org/users/obelisk/6502/instructions.html
Your 6502 CPU emulator would read the next few bytes of the program, interpret the bytes as an instruction, execute the instruction, which involves updating a couple of registers/counters in the CPU, doing some arithmetic or bitwise operations, and possibly loading or storing a byte of data from one location to another. This process is then repeated in an endless loop.
It is a simulation of the fetch-decode-execute cycle.