In regards to mudding - usually the preferred tactic is to use a Big Heavy Fly and work the top end of the mud. Sometimes taking twenty too thirty shot's at the same general area. The Fish will be rooting in the mud and since you cannot see them you just have to hope they lift their snouts out of the sand and see your fly.
If you are talking about "little mud's" or "puff's" you have too follow the string of puff's to the Bonefish (sometimes 300 - 400 feet) - in my experience the little puffs are usually made by "Big Fish" and well worth the stalk.
I have not fished the Key's, even though I live in Florida - The Bahamas are too close, too productive, and cost about the same if you plan on flying from the Tampa area.