Nick,

I look at dealing with negative thoughts this way.  When a thought (a belief) comes into my awareness that is disturbing/upsetting/fearful, I find it best to deal with it like I do in meditation.

I observe it as if I was another person looking in on me and acknowledge it (“hello bad thought. thank you for coming but I don’t need you anymore”).  Then I can let it go (“goodbye bad thought, it’s time for me to get back to my breathing/meditation.”). You can substitute it with the positive thoughts like anita suggested.

Additionally you can notice where the feeling shows up in your body ( gut, etc.) and breath into that part of the body until it dissipates.  I don’t try to push it away.  This way this process incorporates awareness of your body which is related to the issue you are struggling with.  This is part of the acceptance process, i.e. noticing where in your body and allowing that feeling to be there.

Make sense?
Mark