Final Cut Pro

You can create a stereo movie sequence for side by side stereo by doing the following :

Open Final Cut Pro..

go to menu bar FCP and scroll down to Audio Video settings..

then in the Summary tab select the correct preset for your material...

now open the Sequence Presets tab, find ticked preset, check it is correct (as previous step) and then click on the Duplicate button at the bottom of the window.

Now to change the Frame Size..

first click on the Aspect ratio button and select Custom, now double the width of your frame. This will allow you to have both your right and left movies side by side in the FCP viewer.

click ok.

Now create a new Project - menu bar/File/New Project

Now add your clips to this project in your FCP Browser window..

then double click on your first left clip, it will open in the Viewer, in the Viewer, click on the Motion tab, and change the Centre to -X (where X is half the width of your materials frame ie a quarter of your new double width viewer)

Now double click your first right clip, and as above, except change the Centre to X (where X is half the width of your materials frame ie a quarter of your new double width viewer)...

Now you can drop these clips on to individual video channels on the FCP timeline and they should come up side by side in the viewer... you can now sync your clips by moving in the channel.... it can be easier if you go to the bottom right of the timeline window, click and hold down the forward arrow, and select both Show Filmstrips and Audio Waveforms...

... good luck