basically for the speaker to work in best conditions its is always placed in a still air environment.
if the sub is directly underneath a speaker the air aint still so the air flow around the 6x9 is disturbed, therefore altering the expected performance of the speaker.
Speakers are air pistons that move back (on the negative cycle of the signal) and forth (on the positive cycle), creating different degrees of air pressure at different frequencies. The amplifier (either separate or built-in your radio), produces electrical impulses that alternate from positive and negative voltages (AC). This current reaches the voice coil inside the speaker, creating an electro-magnet that will either be repelled, or attracted by the fixed magnet at the bottom of the speaker. The voice coil is attached to the cone, moving it back and forth, creating sound
Hope this helps