But, God is omnipotent right? He doesn't need tools.
See how just a little thought about physics causes you to reject one of the most fundamental claims about God, his omnipotence.
'Little thought' accurately describes your post. It's a clever little turn of phrase that is actually quite shallow and reflects a lack of understanding about what you mock.
For there to be no 'tools' ( laws of the universe) that God used, our entire existence would be magical, and constantly upheld by miracles from God.
This would be proof that God exists, and as such, one would not be free to choose whether or not to follow the word of God, as you would know without a doubt that He is real, He is there, and you will in fact burn in hell if you disobey Him.
Free agency is therefor gone in this scenario, and our existence- the test of what we do with the free will that God gave us- would have no point.
Now, I'm not much of a Christian. I have come to see how much good certain religions have done for humanity, and I see how little atheists have to offer that would do the same.
They offer mockery, derision, and emptiness to counter belief. Judeo-Christian belief (and the nations based thereon) offers charity, fellowship, self-restraint, functional guidance and, oh yeah, centuries of world dominance in all fields.
Humans are not purely rational, and it is fantasy to think the optimal society could be based on non-existent people. Pretending it's even possible requires a certain level of magical thinking.
I would caution you against feeling smug about imagining you're more rational than your fellow humans, as the emotional, irrational side of humanity is what makes everything possible.
There's a certain part of the brain responsible for emotions. If this is damaged, it leaves the rational part of the brain in charge. The result? Such patients are paralyzed by the array of options we face each moment, and are unable to properly analyze their choices- and hence do little at all. (Citation not handy. You're smart enough to find it on your own if you're actually curious.)