With premiere and if you have shot with a dual camera rig, just open the left eye on one video track in premiere and the right eye on the other video track.
You can then play with the opacity slider on any of the video tracks to "visually " match up things for negative parallax or frame drift etc and apply your effects.
One more thing, if you want to avoid headaches and nausea for your audiences, never try to do a cross fade from one scene to another.
If all this sounds too complicated and you just want to produce the regular 3d DVD , try the free and easy to use Stereo Video Maker (google it)
Regards
Clyde
Dubai, UAE