Now that you know have your story ready, it is time to set up your scene. The main goal when setting up your scene is that you have control over everything. First, pick a room that has the least amount of windows. If there are windows, cover them. There are many ways to do this, and two cheap ideas are cardboard or dark fabric.
When setting up it is important that you have a sturdy surface. Always remember that the camera will capture even the slightest movement. Take into consideration the amount of time it is going to take to shoot your movie. Nothing is more frustrating than having to move to a new location and start over because you were in the way.
After you have your location and table set up, start building your scene. You may already have it ready on a baseplate. It is important to tape down your baseplate so that it will not move as you manipulate the characters.
Once the scene is built, bring in the lights and the camera. Position the lights and camera for your first shot. Try using the DC power on your camera if possible because having to change the battery in the middle of a scene will mess up your animation.