How does a Muslim know that he thinks well of Allah or thinks badly of Allah?

He knows that from his ways and his belief in his heart. If he thinks well of Allah, does good deeds, and supplicates Allah, then this indicates that he thinks well of Allah. But if he does not supplicate Allah and does not do good deeds, then this indicates that he thinks badly of Allah The Exalted. The evidences of good assumptions/thoughts about Allah are the actions and the intention in the heart.