I used to focus on just writing the story and encouraging the theme that naturally emerged through that, but recently I've started to think that it's more important to begin with the theme and to write the story around that. It's harder for me to come up with the theme first, but if I don't I end up writing a story more for entertainment than for the glory of God. Preachiness is a concern, but I think if I want a good story I can iron that out, and that preachiness isn't as great a threat as writing only to entertain and for no other purpose.
My themes most recently have been trying to correct various lies. For example, a few days ago I heard netflixs is releasing this movie promoting abortion, that upsets me. So I found every Bible verse that I could about children and birth and I started writing a story around those verses. I don't want to make it preachy, so its going a bit more slowly, but because I'm not writing it just to amuse myself it has a bigger purpose. A reason to be written more than so many other things that I have written over the years.
Hope this is helpful, Suspencewriter.