Your best solution is going to be probably adding the watermark in the encode step. I don't know what you are using, but both Adobe Media Encoder 7.1 and Apple Compressor allow you to do this. You simply save the watermark as an image or photoshop file and load it into the encoder, and save it as a preset. Now depending on a variety of factors (machine speed, video size and framerate, etc) it may be faster or slower than realtime, you will have to test it to find the right formula.