Put on the protective eye wear. Cleaning your popcorn ceiling can dislodge small particles.
Place the drop cloth on the floor below the discolored area. Place the step ladder on the drop cloth below the area you need to fix. Vacuum the cobwebs from the ceiling, being careful not dislodge any of the popcorn from the ceiling. Do not push upward or sweep straight across the ceiling, this can cause the cobwebs to stick to the ceiling.
Brush the Kilz onto the discolored area. Do this gently but thoroughly since this can dislodge the texture on the ceiling. Kilz also comes in a spray paint form, which will prevent dislodging the texture but will drip onto the floor more than painting it with a brush.
Allow it to dry completely before removing the drop cloth. This will protect your floor from any paint drips.