There may be a simpler way, but we just do it in Premiere as a part of our process while we're editing. First we create the main edited version of the video, save it (hi-res AVI), then output it again with the watermark we want and save that hi-res AVI as well. If we're using the same AVI on two websites (there are a few Skyler videos also on Boyfunk, for example) then we just output two versions, one with the Skyler watermark and one with Boyfunk.

Takes a little more space, but disk space is cheap, and if something goes wrong in encoding, or we want to re-encode in a new format, or at a higher bitrate, we don't have to mess with the video at all, just bring the already-watermarked video into Sorenson, choose the encode rates and format, and go.