How do we apply the Stefan-Boltzmann equation to radiative heat transfer from/to CO2 in the atmosphere?
We don't

Emissivity of CO$_2$

Your claim of low emissivity of CO$_2$ is not entirely true. First off, it matters what the wavelength of emission is when determining emissivity. Carbon dioxide has specific bands of high absorption (which correspond to high emissivity). These bands are crucial for climate modeling, so listing a numerical emissivity value without specifying the wavelength is not a useful measurement. 

Secondly, emissivity of a gas isn't as simple as that of a solid surface because solid surfaces are more or less opaque to the IR radiation emitted in accordance with the Stefan-Boltzman equation. Therefore, the surface area of the 'blackbody' is what is important when calculation emission or absorption. For a gas, however, IR radiation will penetrate some distance through it. 

The result is that you need to calculate emissivity of a gas as a function of its optical depth. Staley and Jurica, 1970 present calculations where they do that for carbon dioxide in the 15 $\mu$m absorption band (the most important one for climate models). Their results show that at 20 C, CO$_2$ has an emissivity of 0.0823 at an optical depth of 1 cm; 0.244 at an optical depth of 10 m; etc. 

Spectrum matters

As I mentioned above, the emission spectra matters a lot. In the case of CO$_2$, there is a specific emission band which corresponds to the absorption band. This means that any radiation emitted by CO$_2$ is emitted at just the perfect wavelength to be reabsorbed by other molecules of CO$_2$. 

CO$_2$ also differs from water vapor in that it remains dispersed through the atmosphere and doesn't coalesce into weather formations. Water vapor aggregates into clouds; the emissions from those clouds can be significant because there is much more water vapor emitting in a cloud than in the (drier) air above the cloud. CO$_2$ doesn't exhibit that behavior and thus its emissions are mostly trapped by other CO$_2$, whereas blackbody emission from cloud banks can be significant on the global scale. 

What does get emitted to space and lost is heavily attenuated by the presence of other CO$_2$ molecules and is insignificant compared to emissions from the Earth's surface, which pass through the absorption band gaps in water vapor and CO$_2$.

Conclusion

I don't actually know what factors each specific climate model uses. There may be some that account for the emissivity of CO$_2$. It may be that all the models account for it; it has been over a decade since I contributed to those models. However, whether they account for it or not, it is not a significant factor in driving temperature changes the way the emissivity of the Earth's surface is.