Writing and theololgy

How is it that characters can take over when you start writing? Everyone likes to think that it is a God-like position, writing a story. In my experience, there is no control to be had. I've written three fan fictions and am currently working on the fourth. I might get three or four paragraphs on paper (I still use pen and paper to get going. Composing at the keyboard isn't me. I am SO thankful for recycling.) before the characters take over and do their thing, and I'm just along for the ride.
This leaves me with a rather nagging and worrisome question. What if the Universe was created, and then just kind of had to go its own way? Let's take the existence of God as a given, for the time being, and further assume that he created all that we know, like an author writing a book. If the characters have taken over the whole endeavor, what is the end result going to look like?
When I am writing, things usually work themselves out. The people have defined characters that make them behave in certain predictable ways. I merely give them a situation at the start, and they then resolve it in their own way.
In a situation like this, are we capable of making the right decisions? Story plots are relatively simple compared to real life, and they tend to come only two or three at a time. Life comes at you all at once.
I just hope the Author of our story doesn't develop writer's block.