I would fill the area under the 'egg crate' with rock rubble to increase your bacteria, including anerobic bacteria. Also a nice place for pod development even tough you will lose some to your skimmer.
I posted in your Mag12 question that it might not give you enough flow. However, from your picture you 'appear' to have lots of water moving through your system. Since you already have the Mag 12 see how it goes.