Creating stereoscopic video from two video files
This depends entirely on what kind of 3d video you want.  There are numerous formats for 3d video.  Some are as simple as placing the left and right images either side by side or one on top of the other (typically compressing them spatially to still take up the original space, for example 1080p video done like this ends up being wither 540 vertical pixels per eye or 960 horizontal ones.)  Others involve doubling the frame rate and interweaving the frames alternating between left and right.  Still other formats store the video files separately and stream them in parallel, possibly combined via timecode.  Some even use entirely separate files and just synchronize the players via the timecode (such as with 3d projection with dual projectors).

The split video is the easiest way to do it.  Most of the interwoven options involve special authoring (for things like 3D bluray) and I've only ever seen authoring options for 3D bluray on pretty high end (and expensive) authoring software.  The split option is easy to do and most 3D displays support it, the only downside is the resolution loss and the fact it typically has to be manually configured for playback.  It's by far the simplest and cheapest approach though.