The trick is not to add the watermark on the timeline in the editing app because then you have to export or encode and re-size the video for the end users which results in a slightly less crisp watermark. You are better off adding the watermark in your third party video encoding app like Sorenson Squeeze or Videocharge when you encode the video to the finished format like WMV, Flash etc, and size the watermark at the exact size that you need it.
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