If the energy is used to move something, then by special relativity the object increase the mass [1], and the difference disappears. If the energy is used to heat something, the object increase the mass, and the difference disappears. If the energy is stored elsewhere, also the difference disappears.
The only way to reduce the mass of the Earth (including the atmosphere) is to beam the energy to space, for example using the energy using a giant laser pointed to the sky. A simple solution is to wait until the heat of the atmosphere makes some radiation that escape to space.
Anyway, even if all the energy we produce escapes, it's extremely small, so you can ignore it for all practical purposes.
But it's worse, because the Sun send heat to the Earth. So you have energy going out that decreases the mass of the Earth, and you have energy going in that increases the mass of the Earth. The average temperature of Earth is increasing, so inbound energy/mass is wining.
But it's more complicated because hydrogen and helium in the top of the atmosphere is blow away by solar wind, and solar wind brings some new hydrogen. My guess is that the mass of this exchange is much bigger than the mass of the exchange of energy, but I'm not sure.
[1] Modern books of special relativity don't like to say that the mass increase, because there are some technical problems. If there is no physicist nearby, it's a good approximation.