Knock over means you make the object fall down. Run over means you knock it over and you run/drive/go over it as well. I knocked over the chair. Means I hit the chair and the chair fell. I ran over the chair, means I knocked it over and I went over it and possibly crushed it.

They're certainly very similar. "Knock over" is usually used to describe people, animals or things being caused to lose their balance after being impacted. "Run over" is used more often to describe people, animals or things being impacted by a vehicle, though it could also describe being impacted by a person or animal. "Run over" also often implies that the impacted person, animal, or object was injured, damaged, or even flattened.