You cited the rules in your question.
- Light Cover: A quarter of the target is obscured.
- Medium Cover: Half the target is obscured, or target is prone.
- Heavy Cover: Three-quarters of the target is obscured.
- Near Total Cover: The target is barely visible.
Consistently applying those is a GM skill, that requires paying attention to character locations, relative positions, action descriptions (kneeling behind an obstacle, dropping prone, etc.), and the terrain of the battlefield.
Most game masters find using miniatures, battle maps or 3D terrain, and tokens to mark created cover or changed obstacles to be very helpful when assigning and remembering cover modifiers.
Despite all that, disagreements will arise. I recommend planning how to resolve those before the game, then trying to stick to that plan in the moment.