I was lucky in that my capture didn't have an issue. I captured sound and video at the same time and it was always synced up correctly. On the other hand if you start capturing from different source material I can never see how the person can figure it out enough to make it sync beyond looking and listening at it.
In your case, are you going to sync up your base wavs first? then create the different sound streams based on this one copy of sound, or do it by some other means?