How do I explain to my son what it means to have atypical pneumonia?

An outdated term. Atypical pneumonia is very common (always has been). The designation was used to distinguish it from "pneumococcal" pneumonia, because the treatment used to be different. Now almost all are treated with the same meds. Another misconception is that we can tell the difference by your symptoms and cxr, but it turns out we probably can't. A more useful term is community acquired pneumonia.