There are as many different ways to tone a coin as there are coins - literally thousands. As for how do you tell if it's natural or not - it's a matter of experience. But sometimes, even the most experienced expert can't tell.
i like toned coins but i wouldnt pay more for one because it was toned. the toning is just a bonus IMO, not a selling point.
Ryan coins tone because the metal in the coin interacts with the objects it touches. Even the very air and the chemicals in that air around the coin causes it to tone. In simplest terms, it is a chemical reaction. The metal in the coin oxidizes and that oxidation makes the metal change colors.