The way that I would do this would be to bring all the water marks you want to use into Premiere.
Lets say they are just the watermark and nothing else (no background etc), import them all into Premiere and load each one onto the video. You would then need to go ahead and export or queue as you go, or you could make 50 timelines and queue them all and let it run out all the exports.
You should be able to re position and change opacity from premiere if you needed.
Hope this helps
I should imagine that's the quickest it will be!!