Are the "seven heavens" mentioned in the Noble Qur'an the seven layers of Earth's atmosphere? If not, then what are they, and how can atheists be refuted regarding them?

It is incorrect to interpret the seven heavens as the layers of the atmosphere due to the varying number and intermingling of these layers, and because the religious texts emphasize that the heaven is a sturdy, well-constructed edifice with gates and inhabitants of angels, not merely air or space. The visible part of the universe is insignificant compared to the invisible. When debating atheists, the focus should be on proving the existence of Allah Almighty and the perfection of His attributes, then on establishing the matter of messengers and divine messages as a basis for addressing matters of the unseen.