Sorry for the constant banter, I'm trying to help and figure out this thing at the same time. My sump if very similar to yours. My skimmer has to be in a compartment, so I put it in a separate small tank. Here is how I did that and some of this may be of use to you.
I put an additional pump in the center compartment. That pump feeds my small tank with the skimmer, another separate tank which is my refugeium, and my reactors, each of these has a valve to shut off flow to them. The other two tanks (one small for the skimmer and the refugium) are up slightly higher than the sump and are acrylic. This let me drill the sides and have over flows back into the middle compartment of the sump. Additionally, this adds total volume of water to your system which is always a good thing, and allows for a REAL refugium with a trickle flow that grows pods and such.