Agriculture developed slowly in Mesoamerica. It was not until about 2000 or 1500 BC that permanent farming villages appeared. This is because the yield from cultivated plants was for a long time inadequate to support fully sedentary communities and hunting and gathering continued to make a major contribution to subsistence. However, genetic changes in the maize increased its size and yield dramatically, eventually making it a staple on which sedentary communities could depend.
Beans provided some of the villagers' protein requirements: the rest they gained from game, fish and domestic dogs. (Mesoamerica had none of the animals suitable for domestication, such as cattle, pig or sheep, that existed in the Old World).
Different regions developed differently: our best evidence comes from highland areas like the Tehuacan valley where extreme aridity has preserved plant remains and coprolites (desiccated faeces).
Villages in the highland regions were probably slower to develop than in the tropical areas of the Gulf and Pacific coasts, where bountiful wild resources may have supported sedentary communities even before maize became a staple - but because the humid environment doesn't preserve organic remains we know little about these.