Why not add the watermark in the final stage of editing with whatever video editing tool you're using?

Perhaps I'm missing something, but I'd be afraid that re-encoding the video from source to quicktime to whatever the ending format is could introduce some artifacting into the final product... whereas if you just add it as an overlay in Premiere, for example, before outputting the source file from which you'll be encoding with Squeeze, then it's there in the source file with no added noise from additional data conversions.