Thought provoking video explaining what a scientific theory is:
http://www.youtube.com/watch?v=tUppY9Va3AE
Its interesting to note that Sir Isaac Newton who beleived in intelligent design actually did formulate a theory: The Theory of Gravity in his work the Principia. But then Newton was more of a natural philosopher than a "scientist" of today. He was trying to understand how the mind of god worked out through creation. The great majority of the latter part of his life was devoted to the study of biblical prophecies since he believed the bible to be the inerrant word of God.