I am planning to visit Atlanta in the US from Munich. I also have a friend of mine in Toronto and I see Air Canada and Lufthansa do have halts at Toronto on the way to Atlanta or back to Munich. Air Canada has a stopover program but only if you have a connecting flight between 6 and 24 hours. I see the rates shooting up by 200$ for the same route if I catch the flight a day later, that is, 40 hours later.
Or is there a special way to go about booking such stopover tickets?
That is the price. Anything less than 24 hours is not a "stopover" (there are sometimes different definitions but for an international itinerary, 24 hours is the normal definition). A stop of under 24 hours is just a connection (or sometimes this is called a "layover"). Adding a stop of more than 24 hours often results in either a stopover fee or a complete repricing to a higher priced fare or set of fares.
Of course, this is deliberate. The reason the price is more is that the market will tolerate it (many people want to spend a couple of days in a major city) and the airline's duty is to make as much money as possible for its owners.
There are ways to find good deals with stopovers included. Other questions have been asked about multicity itineraries, it may be worth looking at those questions.
I have no proof, but this is what I always have been told:
They do charge more because the market has proven that people are willing to pay those prices.
The companies that do not charge extra, Icelandair among them, go by the idea that more people will travel with them if they can stay a day or couple of days in their hub country.
The other companies do not see additional travelers or not enough to offset the extra income from those that pay the higher fees.
