Ryan I will let the aeration experts answer that part of your question. I have seen several opinions here on the subject and can find them if you don't get an answer.

On cleaning the rocks I can offer 2 options. One draw down the pond and use a pump and hose to wash them off. We do that with our beach. Another option that will work without drawing down the pond is to rent a pressure washer and an extension (depending on depth of rocks). That will allow you to get the end of the washer about 6in from the rocks. It will wash the dead FA off the rocks. It would need to be attached to a pump from the pond (not chlorinated water). I would assume you could also use one of the pool vac/brushes/sweeper. Not sure how much work that would be at your place.