Unless you have the luxury of having two identical cameras, you'll have to shoot 2 pictures, one for the left eye and one for the right eye. This implies that you cannot make 3D images of animate objects, it will ruin the experience.
Methode 1: parallel
There are 2 methods of getting a suitable images. The first is to make parallel images. First shoot the left-eye image. Then move the camera to the right, but in such way that the axes that go through the lens are perfectly parallel. Do not rotate the camera in any direction!

Method 2: cross-through-center
A better, but more difficult method is to make the axes through the lens cross at the center of the object. Make sure the angle of these axes and the baseline are identical for the left and right image. Avoid any other rotation of the camera, as it will ruin the experience. The more precise you work, the better the result.

The advantage of this method is that it is a closer match of how your eyes work.
Easier way
For smaller objects you can use a much easier method: place the object on a rotating plate, with the center of the object directly above the pivot point. Place your camera next to the plate, and aim on the object and make a photo. Now you have the left-eye image.
Then turn the plate a few degrees to the right, and take another shot. Now you have the right-eye image. And you're done!
Note on distance between shots
The distance between the 2 camera positions is very important. In general, the greater the distance, the bigger the 3D effect. But please take into account that your eyes are 6.3cm apart on average so don't start out with 50cm distance. If the distance is too large, your brain can't combine the images anymore. Only if you want to shoot objects far away, you can try distances of 20cm-50cm. Experiment!