I think you just arent taking Gods word for what it says. Gen 1:1, In the beginning God created...
God says he created. I'll take it thats exactly what happened. Its not putting God in a "box" its accepting what he tells us.
"In the Beginning, God created..."
He set it all in motion...He does not centrally-plan each and every flap of butterfly wings on Earth. We, as imperfect Humans, fail repeatedly to live up to his expectations of us. Of course, all we need do is ask His forgiveness...