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My sump is basically exactly like your design, so I'll tell you some of the things that bothered me and I messed up:
1. Light spill from the refugium causes algae to grow in and around my pumps. This is annoying and I had to clean them much more often otherwise the algae would clog the intakes.
2. When I put enough flow into the refugium so the chaeto would tumble, it would create a powerful enough waterfall to make bubbles that would go straight into the main tank (and worse, right back to the refugium after they'd been chopped up into even smaller bubbles). I also had an issue with the chateo wanting to tumble right into the return pump section. I put up some eggcrate to stop it, but ultimately this made the flow into the return pump section more errant (more bubbles), and lots of algae grew on that too. Ultimately I just really cut down the flow into the refugium and just manually turned over the chaeto which ended up working fine, but I never could find any happy medium where the chaeto could tumble without having additional problems.
3. My return pump area was too small which made water changes really annoying. I wish I had made the refugium smaller and the return pump section bigger.
All my problems were also compounded because I was doing all of this in a 30 gallon tank which was too small for my 120 display, but if I had to do it again I'd have made sure:
1. My return pump area was big enough to allow me to do my most common water change size in one shot. In retrospect I'd have happily sacrificed refugium size for more return pump size. You really don't need that much space if you are going to have a giant ball of chateo in there, it's a very efficient pod factory on its own. I also really hate microbubbles so maybe I'd have put a baffle here too (and if you go over/under from the refugium, the volume would still count towards the return area).
2. I'd have used black acrylic or something to block the light from spilling from the refugium area to the return pump area.
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