Sound waves always overlap (superimpose). But the ear is able to isolate specific frequencies from the superimposed sound waves. Different parts of the inner ear cochlea (a snail shaped organ filled with fluid), and different groups of hair-like cells within the cochlea are (edit: relatively more) sensitive to different frequencies. This allows the sensory organ, and in-turn the brain, to isolate individual notes from the super-imposed wave.
You can find more details here: https://en.wikipedia.org/wiki/Auditory_system?wprov=sfla1
Also check the humans section here, for a relatively shorter and simpler explanation: https://en.wikipedia.org/wiki/Hearing_range?wprov=sfla1
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