Position the tripod and table so that the table takes up roughly the bottom quarter of the camera's frame. Even if the camera will be changing angles during the shoot, strive to maintain at least this ratio of foreground to subject.
Plug the microphone into the camera and place it underneath the table where it can best capture the actors' voices.
Have the people who will be manipulating the bobble heads put the gloves on and duck behind the table. Designate a camera operator work the camera.
Shoot the movie by having the bobble-head people hold the bases of the figures to move the figures while speaking for them. If the camera is positioned right, hands should not be visible, and, if they are, they will be blended into the tablecloth.
Upload the movie onto your editing software, such as Windows Movie Maker or iMovie, after you have finished shooting to edit it and give it music, titles and graphics.