There is absolutely nothing wrong with having evil thoughts, every single person who ever existed had or has evil thoughts. It's acting upon them that make you an evil person.
St. Paul says that we must make up for what is lacking in the Cross of Christ. We must suffer, we must endure temptation, we must love where there is no love. We must put on Christ!
Your bad thoughts or "evil things running through my mind" are temptations from the Devil. Satan wants you because you are a good person who believes in Christ and practises your faith. If you were a bad person Satan would not waste his evil time. When attacked like this tell him, Satan, and all his evil cohorts to go back to Hell where they all belong! [If that does not work...go see an exorcist!]
What is an "evil thought"? Behavior can help people or hurt people, but thoughts cannot. Your thoughts are yours and yours alone! Do not let anyone tell you what you should or shouldn't think.