There are various levels of thinking. At the surface level, you receive input from your senses, analyze the input and make decisions. When you decide to do something, you move to a deeper level, above the subconscious, that triggers action. At this level your thoughts and actions work together. At the surface level, when no decision has been made, there can be a disparity between your thoughts and actions.

       Your thoughts are very important. You need to learn to control your thoughts, both at the surface level and at the deeper level. Thoughts are things. They have a major impact on the environment you create and live in.

      When we say "It is what you do that counts." we are not discounting the importance of your thoughts. We are saying you need to get your thoughts at the decision level to conform to what must be done. Then you do what you think.