It seems to me that one could take a piece of PVC pipe and hold one end on the stain with the other above water. Pour the acid in the pipe, and it would pretty well go directly to the stain. Much safer than being in there with it. It would be more complicated than this for safety purposes, and you'd better be sure you want acid on your pool.

You could even plumb a hose to the pipe with a valve so you could rinse afterwards