You mentioned you were concerned about flooding. A very legitimate concern with sumps when power fails and you get water flooding back into the sump. Looking at the spec of that tank I think it is 20" wide X 18 long. If you lose the top 2" of water and the volume of the overflows your looking at somewhere around 3 gallons+ of water. There's 231 cubic inches per gallon so it's fairly easy to figure out roughly how much will make it back to the sump. Just make sure you have that room in cubic inches above the operating water line in your sump + a bit for margin of error. Freaky the first time you do it, but you get comfortable with it quick.
As far as the skimmer goes, it's nice to keep the water volume so sitting your skimmer on egg crate works well to lift the skimmer. I cut 3" abs pipe to 6" lengths to lift mine then drilled the sides with a bunch of 2" holes so water wouldn't get trapped inside them. With the holes in the side, water flows through them.
To save a bit of room I only put 2 baffles between the skimmer and the next chamber. Personally I think the first baffle in the skimmer section is redundant and unnecessary. This is when I was leak testing mine:
The chamber on the left that's holding water is my skimmer chamber. Notice only 2 baffles. I also only put 2 baffles in the next chamber, but if you wanted your refugium with sand there, you'd have to have 3 like you have in your schematic to hold the sand in place.