If you listen to an orchestra play, all the different frequencies, plus their associated harmonics and sub harmonics, all impinge on your eardrum in a huge mixture. Because the notes played are harmonious, there is no interference. If they play non- harmonious notes, though, you soon notice!
It is up to the tiny bones within your inner ear to transmit these mixtures to the auditory nerve system, and your brain is able to interpret this output as the original music.
Now, all this also happens when music comes from a loudspeaker or loudspeakers, provided they are positioned so the combined sounds are in "normal" relationships.
The speaker cones are rigid, and respond to the electric signals fed them from whatever the source is. In this respect, they are just like those tiny bones in your ear, which are also rigid.
However, like your ear bones, the cones are able to move in a sort of "averaged" manner, producing the SAME mixture of sound wave in the air, as you would have heard directly from the orchestra.
It's hard to explain. But if you listen to a trumpet and a violin, each has a distinctly different sound, even if playing the same note. The difference is that as well as the fundamental sine wave of the musical note, there are harmonics and sub harmonics generated, which mix with the fundamental wave, modifying it to give the unique sound for each. The uniqueness is dependent on the harmonics and sub harmonics present, and the LEVEL of each relative to the fundamental.
You hear the results of the conglomerate of all, as a note from some particular instrument.
So there is NO difference when the sound waves you hear from 2 different instruments mix, as the same sound wave just contains more components!
This conglomerate sound wave is what the loudspeaker cones also generate and impart back into the air, to reach your ears.