The same way you hear in 3D while only having two ears, but reversed.

Your ears are shaped such that when a sound comes from a certain direction, your ears physically alter it in a way your brain can understand. That lets you hear a direction. (Left and right are done by relative volume in each ear as well).

Dolby atmos and similar techniques apply filters to the sound that make it behave similarly to what your ear does, and that fools your brain into thinking the sound came from a specific direction.