The short practices and helpful articles by Elisha Goldstein, featured in this post, help to explain how meditation can help to change our negative thoughts.
Three Simple Ways to Transform Negative Thoughts by Elisha Goldstein
Four Steps to Freedom from Negative Thinking by Elisha Goldstein
Training Awareness Meditation (5 mins): http://www.mindful.org/basic-meditation-train-awareness/
Letting go of an obsessive thought (by Elizabeth Blaikie)
The Mindful Cup of Tea Practice: http://www.mindful.org/mindful-cup-tea/