You really should plot it, outline it, script, and revise, revise, revise it even before you begin to draw.
Plotting- What is the basic plot summed up in two sentences or less:
rough example: character is hungry and makes a sandwich.
In this stage give your self a designated page limit to try to hit around. If it your first story I'd highly suggest no more than a 10 pages one-shot.
Outline- Based off of your basic idea you can outline out how the story goes from point A to point B. What conflicts or obstacles get in your character's way and how are the resolved?
Script it out page for page, fleshing out everything in your outline.
Revise it.
Revise it again.
Have a friend or two or three look at it and revise it yet again. Be sure that they have little to 0 knowledge of the story before hand; that way you know what really makes sense or not to an in-general audience.
Then revise it again.
Thumbnail small, and revise it yet again until your story runs smoothly.
(edit)
Also remember to make your characters to fit the plot. DO NOT make the plot fit to the characters. It really will not end well.
Make the plot first; then make the characters. Also if a character winds up just taking up room in the story and only hindering it, just take them out. That is your way of knowing that they don't belong in it.