I have been running the ecosystem with miracle mud on my 40 gallon tank since October of last year. Don't get me wrong - I love the ecosystem and it's a great place for my macroalgae & pods to thrive!
In February, however, I finally decided to add a Coralife Super Skimmer, and it made a huge difference in my system. It pulls out a ton of gunk continuously (gunk I couldn't imagine being left behind otherwise), and the hair algae problem I had in the beginning is now gone. (Don't know whether it would have gone on it's own, being it was a new system, or not.) I wouldn't go without my skimmer again simply because I've found my nitrates to be much lower since adding it.