There are a couple of ways of doing this.
- take a frame, add your watermark to it, save that frame, repeat the process for all your frames, or the particular ones you want to water mark.
To achieve this there are a couple of ways: - use Image Processing and write a for loop, to get each frame, and add your watermark
OR if you have the Computer Vision System Toolbox, I would invite you to explore System Objects. Use the help and you will see that this makes life easy controlling the frame indexing.
I hope this helps. Gareth