In my mind, putting a sci-fi story in this universe AND dealing with God is rather difficult, or at least gets a bit weird. If you have aliens, you have to think about what God’s plan is for them–did they fall? are they corrupted by sin? does Jesus save them too? I haven’t read C.S. Lewis’ Space Trilogy, but I think it would be helpful for studying Christian sci-fi that takes place in this world.
If your story takes place in a completely different world, then I’d just treat it like Gracie said–like a fantasy world.
Semper ubi sub ubi.