From the Sun. The sun sends out light which is a form of energy. About 32% of the incoming sunlight is reflected (off clouds and the surface) back into space. The other part for the most part is ABSORBED by the surface.

When this energy is absorbed by the surface it makes the surface heat up. This heat is what drives the circulation of air in the atmosphere.

The sun releases radiation, and this radiation adds energy to molecules in the atmosphere. When you hit molecules with radiation, they absorb the energy and become warm, like in a microwave. In the same way, the sun's radiation heats the atmosphere.

When electromagnetic radiation (light) from the sun enters the atmosphere, it can heat up the atmosphere in a couple of ways:

One way is through direct transfer of energy from the light to molecules in the atmosphere. Molecules can absorb light energy and as a result one or more of the following things can happen: 1) electrons in the molecules can get promoted to "excited states" and eventually, when they return to their "ground state" release energy, 2) bonds in the molecules can vibrate, 3) the molecules can rotate (move around some axis) or translate (move along some axis). Because the molecules are moving more, their overall temperature increases (i.e. they "heat up").

Another way the sun's light energy can be transferred to the atmosphere is indirectly. A large portion of the sun's light will make it to the Earth's surface, which will reflect is as both lower energy light and heat. Once the light is reflected from the surface of the Earth, it can follow the paths described above to heat up the atmosphere. I hope that helps!