I think I just realized that they were there right after I had them.

For example, my first question after noticing them is to ask myself why

The important point in your question is using these words: realize and notice. When you realize you are thinking, you are not thinking in that moment. This means that presence has started growing in you. Notice these moments when they occur. Their length is not very important, the important thing is the number of times your insert these spaces in your daily life. For example when you want to turn on the TV and you reach the remote pause for a few seconds while your hand is on the remote. When your doing something in a hurry and suddenly become conscious, stay still for a few moments. These may happen once a day, week or month but as you start noticing them, they grow in length and occur more often.

When you come out of a thinking phase, or a pain body episode, don't blame your self. Enjoy the fact that you can come out of it because many people live their entire lives in suffering and struggling and don't have a chance to get out.

Don't make this into a goal that you need time to achieve. Presence is here and now and its all there is. We just need to stop blocking it from flowing into our daily lives. The fact that your enjoying the book and it makes sense to you means presence has started growing in you.

@Hanna Tanajura -

Simply watch and allow the thoughts in your head to flow and pass without judging them.

Release identifying with the random thoughts. Just allow. Allow. Allow them to pass.

Allow those thoughts to pass (as they will), without fighting or attempting to rid them and you will find (with time) that they will lighten.

Whenever you find yourself watching your thoughts from a "distance" or simply realizing that you are having a thought. You are in the moment.

THE BEGINNING OF FREEDOM is the realization that you are not the possessing entity-the thinker. Knowing this enables you to observe the entity. The moment you start watching the thinker, a higher level of consciousness becomes activated. - Eckhart Tolle

AS YOU LISTEN TO THE THOUGHT, you feel a conscious presence--your deeper self--behind or underneath the thought, as it were. The thought then loses its power over you and quickly subsides, because you are no longer energizing the mind through identification with it. This is the beginning of the end of involuntary and compulsive thinking. - Eckhart Tolle

To question why solves nothing. Even when you know why it solves nothing, you just know why but that is not the answer to changing it. It is like saying while you are driving what is making my car go forwards? Even if you have the answer it will not help you steer the car.

You don't need to know why the car moves to know how to steer the car. This holds true as well for knowing why someone hurt you, even if you knew why it does not change the fact that you were hurt. When we see this we can understand the "Why" is a moot point.

It is information but it is not the information you need to affect a change.

The question is not as much "Why" but "How".

If we go back to the car example, we really don't need to know, "Why the car works" but "How to drive the car" to get from home to the grocery store. I could ask why the car works until we get into quantum mechanics, but it wont help me know how to drive the car.

So to change the question to how to deal with this instead of why this happens I think you will get a more productive answer that you can use.

When you have these negative thoughts think or say out loud, "This is not me! I release this and reclaim my center of peace and love." You could banish it in Jesus name if you are saved, that is another way.

Dear Hanna Tanajura, Don't worry it takes time to master living in the present moment. You are doing fine for a beginner and you will get a lot better the more you observe yourself and put all your attention on what you do.

Don't try to suppress your negative thoughts for they will only persist. It is good that you are observant enough to know that you are having negative thoughts. Just let them be and the best thing to do is to put your attention on whatever it is you are doing.

The first step is noticing that you do this. Be gentle with yourself, don't judge yourself or criticize yourself. Treat yourself the way you would want others to treat you. So first, notice that you are not present, then become present. If you find it difficult, try Two Hands Touching. It is that simple. The more you do it, the easier and more instant it becomes.

Become present, smell the roses, or shampoo, or fresh air, or coffee. Feel the cool breeze, or the hot shower, or the heat of the sun on your skin, or the early morning stillness. Taste your food. Feel the stretch and allow the muscle to to relax.

The more you name the feelings, tastes, sensations, the less present you are, and the more you are in a reality of the creation of your mind. Just experience and enjoy.

The funniest thing about the book The Power of Now, is that I only got less than half way. Whenever I would read it, I would feel as though I would rather be present even at that moment.

All of these are great answers, as to what you can say to yourself, if you have become aware that you have had a judgemental thought, just say "judge not". Then observe the flow of thought and observe the thoughts without judging them. Same can go for feelings. Practice not judging your thoughts or feelings as you observe them. Thoughts about anything, anyone (including and especially yourself), or any place or "situation". Do some reading on Mindfulness meditation and you will learn a lot more about observing thoughts and feelings without judging them. It will take practice and you'll become more aware with practice.