A lot of prominent writers (the ones who land traditional pub deals, go on talk shows, get to see their books become films…) tend to write with deep meaning between the lines. A writer can use ways to create meaning behind the face value of the story using symbolism, their protagonist, and general commentary on society outside of the fictional tale.
Research becomes a writer’s best friend in this scenario. When research is applied to the writing, particularly in the setting, creates meaning for the story as a whole. Knowing where your story will take place will help narrow down symbolism as well. Check out folklore, mythology, any literary history of the country you choose. Even names contain meanings sometimes.
You also have to keep in mind that your subconscious will become more apparent in your writing and the only person who will notice is you.
Re-read your draft and see if you’ve executed the story and given the deeper meanings justice. And if you haven’t, well…what are you waiting for? Get back to it!