The deeper meaning of a story comes up out of the story itself over time. Thus, the Thematic Significance plot line is generally saved for the last or ignored or overlooked all together.
The more aware a writer is about their own personal themes, the more attuned the writer will be in the search for deeper meaning.
Shana Mahaffey author of Sounds Like Crazy begins writing with theme on her mind. I recently interviewed Shana about her plot process. Read more about this up-and-coming star who is currently working on book two of a two-book contract from Penguin Group, the second largest trade book publisher in the world behind Random House.
For more on theme: