For most studios, the film is visualized and composed normally, then the "flat" version is used as the left eye of the stereo version. An additional set of render passes is made for the right eye using an offset camera (sometimes, if you're creative with compositing you may not need to do an actual render). This process also allows a stereo version to be created relatively cheaply if the client decides they want to do one halfway through production...
Source: Worked on several stereo animated and live action features and designed stereo compositing versioning process.
Source: Worked on several stereo animated and live action features and designed stereo compositing versioning process.