is your skimmer a
HOB or inline?
If you can put the skimmer outside of the sump, and just plumb the return back in, thats what I would do.
I have almost the same design as yours and I have my skimmer pump in the 1st section and the return into the 2nd. My heater, probes, float valve for auto top-offs and return pump is all in the last chamber. I got mud/macro algae and
LR rubble in the main middle section. Bioballs and filter floss in the small section between the "fuge" and the last compartement to keep the algae from getting into the last chamber and getting pumped back to the main tank.
you'll probably only need an inch or so of sand/mud and you should be able to run the sump at half full or so....