Use the Split Video function in
Auto Movie Creator to synchronize the start time of the Picture-in-Picture transition.
As an example, add your video to the storyboard and right click on the clip in the storyboard. Select 'Split Video' and split the video where you would like your picture in picture to begin. Click 'Add Splits to Storyboard'. Put the next video on the storyboard and place the picture in picture transition between the two clips.
More information on
splitting video is available here