With such cool program as Magix Movie Edit Pro its pretty easy to synchronize and align stereoscopic video.
I show you how:
The whole process is simple:
After you add video of both cameras in time line and select it do this:
Then to that:
Here you can see the final result of adjustments:
Some times you need to find the good position in video to use auto align for better result to start manual correction.
Also before all i prefer use plugin Deshaker with VirtualDub Batch Assistant, from no its best stabilized plugin for VirtualDub i ever seen! And its FREE! =)