A ton of ways.
First, as you said, commercial aircraft fly in designated “sky highways,” which are separated both horizontally and vertically, so at cruising altitude, planes in the same “highway” don’t cross each other. Planes follow their designated flight paths by some combination of GPS, inertial guidance, radio beacons, and other waypoints.
Second, crowded airspace is monitored by air traffic control. Controllers can see the locations of all the planes in their designated areas and can make sure planes keep proper separation and alert pilots to be aware of other planes or to make heading or altitude adjustments to avoid getting to close.
Third, pilots can talk to each other on radio to keep each other aware of their locations, headings, altitudes, and speeds.
Fourth, most planes have some sort of collision warning system that can automatically detect other nearby aircraft and in some cases, even maneuver the plane by itself to avoid a collision.
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