I'm sure that somewhere out there someone else has come up with this, but I figured it out on my own quite accidentally a few months ago. Some of you may know that I'm not super stone/crystal knowledgeable. I have only recently really started a collection and began to learn about them, etc. Ok, moving on. I also have horrible insomnia and I was plagued with nightmares for a long, long time. A while back, I decided to use one of my newish amethyst stones to help me sleep. I began by just holding the stone, and then my intuition or something took hold and led me from there, so now every time I need to calm down, or release any type of negative feeling or overwhelming feeling, I grab a stone and meditate with it and this is usually how things go...
I sit and try to clear my mind, but usually when I need to do this, that proves to be very difficult. I have no idea WHY I see things in my third eye this way, but I do: I visualize the emotion I'm feeling as a color. For example, if I'm angry I visualize deep red. I see it in my mind, coursing through my body and I focus on pulling it in to the center of my body, in a ball of colored energy. After that image is clearly in my mind, I can feel the energy pulsing and I slowly see it forming a river of energy through my arm, and ending by leaving my hand and entering the stone. I continue this visualization until I feel totally calm and my mind is clear and I'm certain that the emotion I was feeling is gone.
I usually try to cleanse my stone shortly after doing this, but sometimes I don't feel it's necessary. Stones can hold a lot of energy without it leaking back out from my experience, but I don't like taking chances, usually.
I don't always use amethyst. I generally think about the emotion and select a stone that will help counteract that feeling.