For a beginner, the simplest way to do it is use two cameras (note the cameras should not be so thick that interaxial distance between them is >> than the distance between your own eye.
Ofcourse the distance between the cameras differs depending on the difference between the camera and the objects in focus. For distances upto 3 inches, the closest object is 10 feet away else you start seeing double images. To get close ups one need to design a rig so that the distance between images captured by the two cameras is not dependent on the physical model of the camera.
We designed our own rig for it- details soon.
Also there are lots of distance calculator available online- one is stereo brain but one has to pay for it but it is a pretty good software - you can have trial version for 15 days and play with it.
Handy Tip: Remember to use the clap - you would need it to sync the two videos.
Once you have two footages - one for each eye - export them to fcp and read the instructions in the following link to merge it:
http://www.dvinfo.net/forum/3d-stereoscopic-production-delivery/97687-3d-anaglyph-plugin-filter-fcp.html
Basically - we remove red from one imae and blue and green from another image.
Btw here is the 3D glass I made:
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