Create 3D movie clip from .MOV footage (20 seconds)

I have 2 .MOV clips of about 20 seconds. They are filmed on identical cameras mounted eye distance apart. I need them editing together in 3D format options to see which works the best. Please only respond if you have experience editing 3D movies together because I need to understand what the best options are. This is a prototype to be followed by more movies that are 5 minutes in length.