Ok, so imagine using those pins in 3d, 3rd person view, with a look similar to PS2's kingdom hearts or the new kid icarus's land battles. That'd be cool, right?
Now, you would see both battles on the top screen, with your interface instead on the bottom. No, the screen wouldn't be split up-the game plays both realities at the same time, ONE FOR EACH EYE. There wouldn't be 3d, of course.
For example, if you were to close only your right eye, you could see Neku fighting. If you were to close only your left, you could see Shiki. Having both eyes open would have you see both fighting at the same time, in the same place, which would be similar to paying attention to the top and bottom screen at the same time in the original.
If both of your eyes were open, it might look like this.
Otherwise, your left eye sees Sora and your right eye sees Kid Icarus!
I hope that made sense.