Since I am not in the academic business, I enjoy the distinct pleasure of constantly leaping from philosophy to theology and back again. Here are some musings...
The two disciplines are distinct. In C. IV of Leisure, the basis of culture, Joseph Pieper provides a good distinction between the two. The best discussion of the relationship of philosophy with theology is, of course, Fides et Ratio (Faith and Reason) by John Paul II.
Philosophy cannot rely on truths revealed by God; that is, it must rely on reason alone. In theology, reason works with the truths of revelation (therefore, it presupposes faith).
Philosophy strives to acquire through reason what has been revealed by God: e.g., the existence of God, the human condition, the way to happiness, etc... So, why philosophize, if these truths have already been revealed and are accessible to faith? Why seek explanations when we can just accept everything on faith?
Well, revelation and theology give us a clue about the true, the good, and the beautiful, but not rational proofs or fully articulated ideas. The philosopher, because he loves wisdom and seeks truth, desires the knowledge of the theologian. He will never fully explain the truth or exhaust its possibilities. But in pursuing with his intellect the truths offered by faith, he becomes more human: out of a desire to know, he exercises that which is in him most distinctly human, his reason. And by seeking to know more of God with his reason, he enters into a personal relationship with the Truth (because faith tells us that God is personal).
Faith and reason are distinct, but are completely in harmony. When reason purports to give a comprehensive account of reality--abandoning faith--it becomes corrupt. But when reason pre-philosophically submits to truths of faith, it gains an infinite field of inquiry and wonder.
Every human being has pre-philosophical assumptions; every scientist brings a pre-scientific credo to his laboratory. What matters is what those assumptions are.