Create a head for your stabilization gear which can house two cameras instead of one. Whether you are using DIY stabilization gear, or professional gear, this is crucial in creating a 3D image. The spacing of these cameras is crucial as well. The distance from the center of one lens to the center of the other should be 2.5 inches. This is the average interocular distance, so it will recreate the way the eyes see. This is a good reason to use small cameras.
Attach the cameras to the stabilization gear. Typically, you can think of the human pupils and retinas as facing straight forward, so this is how you want to arrange the cameras. After a few attempts, you may want to experiment with facing the cameras slightly toward or slightly away from each other to compensate for the overlap in the eyes. Different cameras have different crop factors, so see what works best for your method.
Record the footage you want. Make sure that you start both cameras rolling and then give a way to sync them up. You may try to do it based on the action in the scene, however using a slate or even hand clapping (on screen) once they are both rolling is an excellent and quick way to sync them in post.
Upload and log all of the footage. Organize the footage which came from the right camera and that which came from the left. When you go to edit a scene, be sure to sync the right and left cameras and edit all the action how you want it. Then place the footage from the right slightly to the right of the screen, and the footage from the left slightly to the left; you will be adjusting this placement later. Set both opacities to about 50%.
Tint the footage on the right blue and the footage on the left red. It's only a slight tint, but this is the standard organization of 3D glasses, so once you have both of these, the glasses will help your brain recombine the image and it will look normal.
Put on a pair of glasses and admire your work. If the color is off, lessen the tint just a bit. Also, try adjusting the placement of the right and left camera. If it makes the effect worse, move it in the other direction. Keep trying and tweaking until the 3D looks as good as you can get it.