Put any identifying label or mark on each camera in any way you want. You may instead put the identifying marks on the cameras' memory cards, especially if you will transfer the footage through the use of a memory card reader. This is to avoid confusion on which footage is supposed to be on the left and which one is supposed to be on the right.
Set up the two video cameras to record the left and right frames. You need to make a 3D rig to be attached as a plate for the tripod so that the two cameras can share the same height from the ground and a certain distance away from each other. Another option requires a tripod for each camera. However, it is important to make sure that both tripods and cameras are on the same height and "looking direction."
For an amateur video, the distance between the two cameras should be anywhere from 2.5 to 20 inches. The best distance depends on your kind of shot, which is quite technical. For professional 3D projects, the mathematical and creative decisions involved in this are parts of the job of the stereographer.
Shoot the scene simultaneously using both video cameras. Give enough time allowance when you press the "Record" and "Stop" buttons to ensure that you complete your intended coverage for the shot.
Ideally, for more professional works that use additional gadgets and prosumer or high-end cameras, a remote control device is used to sync both cameras when pressing the shoot button or zooming in or zooming out. If you don't have these resources, the best way to still sync the left and right footage is to use a clapperboard when shooting. Include the sound coming from the clapperboard so you can sync up the sound and visuals for each footage during postproduction.
Transfer the footage from both cameras either by connecting each camera to the computer through a USB or FireWire cable or by using a card reader.
Make separate folders for the "left" camera footage and the "right" camera footage.
Open each corresponding left and right shot in your 3D conversion software. Many free programs are readily available for download. Depending on the program used, follow the steps on how to apply certain adjustments required for the conversion until you begin processing your final 3D footage. You need anaglyph 3D glasses, also popularly referred to as the red-cyan glasses, to view your 3D movie.