Kepler and Newton came up with orbital equations and gravitational theory that explained the movement of the the planets. Using gravitational laws we can predict the movements of the moon around the earth to great accuracy.
But the moon does not orbit the earth because of these equations, the moon orbits the earth and these equations describe the movements.
God set up the universe to function how it does. But God also sustains it, this means that it is not wound up and would run without him, if God removed his sustaining power the universe would instantly cease to exist. Anti-theists complain that this means we cannot do science, that we are at the whim of a God. Well we are dependant on him, but that does not mean that the universe is irregular and unpredictable. Leaving aside the fact that an atheist view of the universe gives us no reason to even trust our senses, if God is not capricious, then we can rely on his usual providence. We can therefore examine the universe with an assumption of a constant God who set up the world with a high degree of predictability.
This predictability has been known by all cultures and predates the scientific method—the scientific method gives a tool to gain underlying knowledge and make predictions based on models. As the earliest scientists said, they were thinking God's thoughts after him. Isaac Newton stated,
This most beautiful system of the sun, planets, and comets, could only proceed from the counsel and dominion of an intelligent Being.Because God sustains the universe he can manipulate it at his will. Not that he necessarily does this on frequent basis. This intervention we refer to as (specific) providence if God's hand guides specific events according to his will, or even at our request; we refer to it as miracle if it involves the overriding of physical law. Both the general upholding of the universe and a specific change to how the world usually operates are of equal ease for him. If God can stretch out the fabric of space then the multiplying of loaves and fish is of little difficulty.
That is why science is unable to disprove miracles. Miracles are not within the domain of operational science. Miracles are God's specific activity, not his general activity. We cannot observe regularity in miracles to formulate physical law. However they are provable, just via another method: testimony. Proof of miracles is via witnesses.
Miracle is also proof of the supernatural. Science can say the the world operates "like so" under the normal scheme of things. Observations that contradict what we know may be due to miracle and science can say nothing against it—science does not describe specific providence, only the general. Dead men do not come back to life according to biological science, but there is nothing to prevent God doing this in a specific case if he so wishes.