I just got done making a sump out of acrylic and I did mine pretty much the same as yours. What I did was put the inlet area for my protein skimmer -- drilled a bunch of 3/16" holes from 4 - 6 inches up that leads into the refugium area. I drilled another bunch of holes at the 10-12" mark for the next divider. 2" away I added another baffle but raised it up 2" off the bottom for the bubble trap. It was nice making it out of acrylic -- bought the pieces cut to size and made it as big as possible to fit under my cabinet. Was able to put the protein skimmer and heater in. The plans I used for mine was the model K sump from Melevsreef -- Melevsreef.com | Acrylic Sumps & Refugiums
I made an overflow box from his direction but I get a few bubbles that build up in it and have to suck them out every so often. Not sure how to completely fix that yet.
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90 gallon with 26 gallon sump/refugium, 2 x 250 MH lighting, 100lbs live rock, 1 - yellow tang,1 damsel, 1 - cleaner shrimp, 1 - coral banded shrimp, 3 - emerald crabs, 2 - porcelin crabs, 6 - peppermint shrimp, 1 - green ricordia, 1 - toadstool, 1 - brittle starfish, 1 - sand sifting star, 100's baby feather dusters,Ass mushrooms, frogspawn, xenia, 1 clam,
6 - Leather coral, Green star polyps,Lime green/orange button polyps,1 huge carpet anenome,various snails/hermit crabs | 
