MCUs are Modular Components, defined in MCU definition files representing different modules inside the MCU as: cpu, memories, I/O ports, timers, etc.
To do a Microcontroller simulation just pick the Microcontroller you want from the left panel and drop in the circuit, then build the circuit you need to test your firmware.
When your circuit is ready, Right-Click on the Microcontroller and select "Load firmware".
Select an .hex file to load to the Microcontroller.
If no error message is shown, it means that firmware was properly loaded.
Microcontrollers in the simulation don't need a clock connected. The clock signal is always generated by the simulation.
To set the Microcontroller clock speed:
By default clock speed is set to 20 Mhz for Pic and 16 Mhz for Avr and Arduino.
Now you are ready to power the circuit and watch the simulation.
This is the Microcontroller's Properties dialog.
These setting are equivalent to configuration bits (MCU Fuses).