How does God’s sovereignty work together with human choices?
My answer is that I do not know exactly how this works. I just know that it does because the Bible so clearly demonstrates that God gives us sovereignty over our own choices. We have free will. He does not force us to obey him or to believe in him or to repent of our sins. I could give you literally hundreds of passages that prove this beyond doubt. Joshua told the people to “choose this day whom you will serve,” and Moses told the people in Deuteronomy 30:19-20, “This day I call heaven and earth as witnesses against you that I have set before you life and death, blessings and curses. Now choose life so that you and your children may live and that you may love the Lord your God…” That God gives us a choice is clear, biblically. How he does this is that in his own sovereign choice he made us that way. His sovereign will as Creator was to give certain of his creation sovereignty within their own sphere. Animals and inanimate objects do not have such choice but humans do, as proved from biblical passages and human experience.
Let me use a human analogy (although human analogies can be very limited to explain godly realities). There are two kinds of executives. There is the kind who controls everything from the top. All decisions go through him or her. No one has permission to do anything not directly authorized by this executive. This is the Calvinist God. There is another kind of executive who sets the company in its general direction and gives broad goals and vision to the workers, but who entrust the local decisions to them. Not only does he or she give them authority in their own sphere, he promises that he will back up their decisions. The choice is theirs and his is to provide the resources and broad vision and to let them act. (of course, this analogy is limited because in our world there are consequences for rebellion, unlike my theoretical company)
The God of the Scriptures is the second kind of executive, as is clearly illustrated by the Bible. Exactly “how” he does this–what God “does” to give us this self-awareness and ability to choose—even to choose to rebel against him, I cannot say the process he uses to do this. He is, after all, God.