Determine the theme/lesson the story teaches. Determine what story style was used to present the lesson. (Talking animals? Fable. How something came to be? Just so. Out-of-sight heroism? Legend/Folklore.)
As far as Jonah and the big fish: Could be true, might be metaphor. Either way, we learn that Jonah was in a dark place when he disregarded the words of the Lord, and emerged into light once he decided to follow them. Is there truly any benefit whether the dark place was in the belly of a fish, or simply a dark place. It appears that Jonah's shipmates thought he brought bad luck. Was it possible they tossed him in the belly of the ship, the brig, until they came ashore and evicted him from the ship? How would where Jonah spent the three days change the story of him turning from disobedience to obedience?
Those of us who have experienced miracles in our own lives, are not quick to dismiss miracles in the lives of others. What purpose does an atheist have for picking a story apart? Is s/he looking for the lesson/theme, or is s/he searching for an excuse not to believe? Let every atheist know: You are excused from believing. Move on while those who remain behind discuss the theme/lesson.