Why do clouds seem to be flat underneath?

Most large puffy clouds (usually ulus) do have flat bottoms and this is determined by the dewpoint temperature. Called the "ceiling", the flat bottoms of the clouds indicate the exact altitude at which dew point temperature is reached (where condensation of water vapor occurs). You may also notice these flat cloud bottoms tend to be closer to you on rainy days and farther from you (higher up) on nicer days. If it is rainy, the dewpoint is close to being reached right at the surface of the Earth, bringing the clouds closer to you. If it is clear, the dewpoint temperature occurs at a much higher altitude, pushing the clouds higher in the air. So to answer your question, it has more to do with moisture and dewpoint temperature than atmospheric layers. Hope this was helpful.