The atmosphere is heated in several ways - heat from the core of the Earth, by radiation from the Sun, conduction from contact with warm land and water, convection to even out the temperature and by absorption of infrared radiation from the warm land and water.
The core of the Earth is very hot. It is nearly as hot as the surface of the Sun - about 6000°C. The thermal energy of the core is transferred to the surface of the Earth and the lower levels of the oceans by conduction. Water in lakes and oceans transfers heat to the surface by convection.
Most of the radiation coming from the Sun passes right through the atmosphere, because the wavelength of visible light is not absorbed by the atmosphere. Only the long wavelength infrared portion of sunlight is absorbed, and this heats the air. Convection then spreads and evens out the heat.
Air molecules that come into contact with the warmer surface of the land and surface of the oceans and lakes increase their thermal energy through conduction. Those molecules then heat up other air molecules through convection. In the winter, the land and water is relatively cooler, and so the air is cooler, too. Since the land and water are relatively cooler in winter, they do not emit infrared any radiation to heat the air.
When land and water become warm in summer, they emit long-wavelength infrared radiation that is readily absorbed by the atmosphere. This continues during nighttime, too. Convection in the air then spreads out the thermal energy throughout the atmosphere.
As noted earlier, the warm surfaces of land and water radiate infrared energy. Most of it passes through the atmosphere and is lost to outer space. Some of that energy is absorbed in the atmosphere, thus heating it. Under normal conditions, the amount of thermal energy heating the Earth and its atmosphere from core heat and radiation from the Sun is the same as the amount lost into space in the form of infrared radiation.Thus the Earth's average temperature stays relatively constant, and there is equilibrium between input heat and heat lost.