Yes I have! For amphidinium dinos and I have found it to be somewhat more effective. I would turn my pump off when dosing for about ten minutes, use a syringe to inject right into the sand. Everyday I would target a new area where they were popping up.
I tried, but it was difficult to get it to go directly into a specific area of the sand bed. But, increasing biodiversity in your system seems to help fight against dinos. No proof, but I would suspect shooting peroxide directly into the sand bed would probably harm the natural flora in the sand bed and therefore, possibly hurt in the long run.