sounds like you are doing a stereo pair…something I have worked on quite a bit in blender
I even made a stereo pair seq plugin a long time ago to make it really fast and painless to make either a Xeyed or relaxed view stereo pair. If you are interested in checking it out, let me know.
If you want to do it with nodes, here is what I do…
Open blender and delete the everything in the default scene but the camera. Then set your render settings so that the x size is 2 times the size of your R & L avi’s. This is to get your output size set right.
Add a couple of image nodes, one for each of your avi’s. Add a translate node for each and then alpha over the render layer output.
here is a screenshot of a couple of old avi’s that I made a couple of years ago that I just set up (I used my plugin back then…) the avi’s were 120 frames, 320x 480 and the render setting is 640 x480
BTW: the avi’s were rendered from an old fireworks tut blend - not my own work