Write a page or two-page synopsis to help you define the core story you're telling and the allegory the story. Stephen King used a lot of religious metaphors and allegorical passages to tell "The Stand." On the surface, the book was a simple story of survivors in a world nearly destroyed by a virus. The subtext of the story was about the battle between heaven and hell, good versus evil. Before you begin, a clear-cut delineation between the literal and symbolic stories you want to tell will help keep you on course.
Write to a theme. A town battling against raging fires is a surface story on its own. Using the fires to represent nature fighting back when modern progress tries to move in is not only allegorical, it's a statement. The theme is nature versus man. The fire represents more than fire. It represents nature's need to win out.
Create characters and situations you can use as literary devices themselves. The people of a town called "Hope" coming together to save the town from being destroyed would stand as a symbol to both the theme and the plot of the novel. Show the characters of the town, through their everyday roles, taking on actions that relate to the theme and plot as well. For instance, a mysterious stranger arrives to the town who has the ability to lead people. This character could be related to many fictional and historical figures and be used as an antagonist or protagonist.
Tell your story in a way that keeps readers entertained and gets your message across without being overbearing. A good allegorical novel can be read easily on both levels. Write the literal story so it is enough for a reader who doesn't look for hidden meaning or message. That story should stand on its own. Write the deeper story for those readers who enjoy analyzing. That story will need the surface story for support. Blend the message you present with metaphors and symbols with the literal story. Readers looking for the deeper meaning will read your passages thoughtfully to determine what your story is really saying.