The simplest way to do this is to create left and right movies to run on 2 outputs. Sync 2nd to first.

Another way is to create a movie twice the width with left half the left and right half the right. With new Mac Pros and solid SSDs, 3840x1080 (2 1920x1080) sized content runs fine. Set mix one with a left offset for the layers and mix 2 to a right offset for the layers.

Another trick but requires good network is to create all of your left pieces and right pieces with the same file numbers. On Left machine point to the folder for left. On right machine point to the folder for right. Now run the second machine as a remote of the first. The beauty of this method is that you program only one machine but the media is running from two.