I would love to see LR have the ability to add more than one watermark preset. I know there is a 3rd party plugin, but it a tad cumbersome to set up.
I have had situations where I used Watermark functionality to include a corporate logo in each corner of the image. In those cases, I created the Watermark PNG file to have all four logos. As long as your watermark graphic and your output images (and their associated crop) are the same Aspect Ratio, it works reasonably well.