How to transfer simulation to the Arduino

You'll have to write a native.cpp file for your simulation. It contains the I/O assignments and some boilerplate code for the arduino such as the setup function and the main loop.
A good example is the native.cpp that is in the simulations/arduinoTrafficLights directory.
Just use that as a basis and change things appropriately for your board.

You can copy any Marker to or from a digital pin and copy any Register to and from any analog pin.
Don't insert any sleeptimes in your loop! Use SimPyLC's timers instead.

Jacques