Hey there, I'm a real live nuclear physicist, and I can tell you that atoms are not real, and god certainly didn't assemble them. As far as I can tell neither got nor atom 'exist' in the 'reality as we know it'.

Both god and atoms are merely models that describe the behavior of a system we don't understand. The god model is very nice because it requires very little thinking or participation from the user (believer). E.G. Q: how does chemistry work to produce a poison or a medicine? A: God will heal you, and works 'in mysterious ways' or conversely A: There are many different atoms and molecules that we can differentiate between, and lucky for you we know that some are more or less toxic then others and some might even help you in X, Y and Z ways.

The atom model is more difficult, it requires much more thought, critical thinking, logic and working memory. The chemistry model is also very powerful, results occour in 'real' reality and are repeatable. The god models is easy, because you only have to remember the one answer that works for all cases. The god model is also very weak, there is no effect of merely believing in an outcome, regardless of what you measure.

Of course no one is going to force you to learn chemistry, physics or math, and that's fine, if your model of the universe does not include science, calculus, logic etc, then you'll just have to get by with out it.