Typical means what you would expect—a typical suburban town has lots of neat little houses and people. Atypical means outside of type—an atypical suburban town might be populated by zombies in damp caves.
Atypical is a synonym of "unusual," but it carries a more objective feel—scientific studies might mention atypical results, suggesting that there is a clear definition of what is typical and what is not. "Unusual" is more of a casual observation that one might make in a non-scientific context.
