Sri Sri Ravi Shankar:
Never mind. Thoughts are thoughts. As long as you are aware that these thoughts are coming, you are very safe, because these thoughts come and go.
Negative thoughts come due to several reasons:
1. Lack of good circulation in the body, and improper proper breath or not enough oxygen supply to the brain.
2. Lack of good bowel movement; if you are constipated, you can notice negative thoughts coming.
3. Low prana or no energy.
The remedies for this is:
1. Improve circulation. Get up, do your exercise, sing, dance, do yoga, meditation, pranayama; all these will help.
2. Do some cleansing once or twice a year. If you have not done Art of Living Yoga Level II, where you learn to drink water and cleanse your whole system through Kunjal (cleans the throat and the stomach) and Shankha Prakshalan (cleans the complete elementary canal, from mouth to anus), you should do it.
When you drink a lot of water and do a set of exercises, the water will cleanse your body and flush out the entire system. This is the reason why yogis advised these kriyas since ancient times. It has helped many people to clear thoughts.
3. Keep good company. Company can also pull down your energy.
In spite of all this, if you get negative thoughts, never mind, as they come they will go. If you get scared of them, they will stay with you. If you are not scared, they just leave you.
I am not discouraging you from praying. Prayer can precede meditation. You can pray, and then sit and meditate.