The notion of primary and secondary causes is essential to understanding the role of God in creation in the context of our modern world. Although I had heard these terms before, it was from St. Thomas Aquinas that I got a clear picture of what they mean.
God is the primary cause of everything. This not only means that God caused things to exist at the beginning, but he continually causes their existence, and gives them the ability to do what they do. This idea appears in Scripture: "In him we live and move and have our being" (Acts 17:28, where Paul is actually quoting a pagan poet), and "in him [Christ] all things hold together" (Colossians 1:17).
All of the matter and energy in the universe is caused to exist by God. If God were to cease causing them, they would cease to exist. Particles of matter and energy have the ability to interact with each other, and so they act as secondary causes. These secondary causes act not only at the level of physics, but also at the chemical, biological, and human level. I might say something that causes someone to do something that they would not have otherwise done, for example.
Everything that is studied by modern science is at the level of secondary causes, and science has done a good job of describing how these secondary causes appear to interact. However, nothing that science has uncovered has affected the philosophical need for a primary cause, nor has it found anything to disprove it. The concept of a primary cause is metaphysical, and outside the bounds of modern natural science.