There's a few ways to go about it. Either the screen will display the left and right images polarized simultaneously, and the polarized glasses will sort out which image goes to which eye. Or, the left and right images will be interleaved frame-by-frame, and shutters on the glasses will select which eye gets which image.
The best option is no glasses. You know those holographic posters where the image changes as you walk by it? It's exactly like that only the image changes every 3 inches, so each eye is guaranteed a different image (only in this case it's not a movie poster, it's a movie).