The story should be set in your head before you write your story. The characters and how they will interact with each other should be settled in your mind as well. Now to keep it all strait you should write a treatment, and make notes. A treatment is a short story, a plot and character guideline. Notes will keep your character in line too.
I was thinking about how to illustrate short story treatment plotlines, and this is what I came up with is this. Two bushes spring up from the same root bundle. Seeming to have two distinct beginnings, they grow and the resulting branches become intertwined, tangled and fighting for their place in the sun. In essence, the same battle is going on underground within the root bundle, for water and food. This is a vision of plots, motivations, and sub-plots, and hidden motivations.
Your characters will naturally split into at least two camps, protagonist and antagonist, in simplistic terms the good guys, and the bad guys. There is a third type of character, the anti-hero. The anti-hero is the wildcard character in a story.
As in nature you cannot have a fully dimensional story, as you cannot have a bush or plant without roots. Not exploring the root cause of tensions, or attractions between characters leaves you reader hanging. Your readers are like most people, they want to know everything. The idea is to keep the reader guessing about the plots and sub-plots. To keep it all strait, you need to write a treatment, and make notes.
It is the writer’s responsibility to present the fictional facts, and not get the reader bogged down in details. Suggestion as to what is happening is actually a lot stronger than exhaustive details. Leaving the filling in of the details to the reader’s imagination makes the story more entertaining to the reader.
For example: when I was home from school during the summer, I would occasionally sit in on a meeting of my mother’s book club. I noticed that most of the discussion was about this character and that character and what they were up to in the book being discussed.
I read the books being discussed and discovered that the actions and motivations of the character being discussed were not actually written in the book, only suggested; a fine example of the powers of suggestion. The actions of a particular character in a story need not be graphically overly described to be effective. In fact a tactic that I have come in contact with is to set up a situation, and before anything happens, the story moves on to another sequence. We can find this type of suggestive writing in crime novels, and steamy romance stories. Let the reader’s imagination fill in the graphic details.
You need to keep that treatment handy and make good notes. They will be your map through the story as you write it.