Both explanations, if properly understood, are not contradictory.
God is the cause of every natural event which we see. But He is not directly causing each instance of them; He has created the natural world with laws, with ordering principles, which stand as secondary causes.
The First Cause is God. But natural science does not study the First Cause, and thus it doesn't need to constantly refer all its findings to the hand of God. It studies secondary causes, the natural causes of the events we see.
I let go of a pencil. It falls to the ground. It was not God who directly took the pencil and took it to the ground; He has estabilished in the universe, in His creation, certain constants, a certain order, according to which bodies attract each other, and this explains why my pencil fell.
Other religions, like Islam, have a great problem with this kind of thought. According to some Islamic thinkers (in the Middle Ages; I don't know how islamic thought developed since then) it would take away from God's sovereignity to posit any secondary cause. Allah's will is the direct cause of everything, and just as my pencil fell last time I released it, it may go up the next time; it all depends on the will of Allah, which is completely unknowable to us.
With such a theological view it is no wonder why Islam did not develop natural sciences.
On the other hand, experimental science began in the Middle Ages in the West, where Catholic thinkers and philosophers did not have any problem in realizing that God created an inteligible, ordered universe with constant principles, which we can discover and elucidate by means of observation.
To disregard science in favour of God's will is an error, in fact an anti-Catholic error, that is, contrary to the spirit of Catholicism, which always in the most perfect manner conciliates reason and faith.
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