Quick and dirty way...
3 chamber
chamber 1 - return & skimmer, this will be your filtering chamber, the constant height on the water makes your skimmer stay constant.
Chamber 2 - Refugium chamber- This is where your macro algaes and other things will live.. personally I also like keeping "weedy" corals in this area (yellow polyps are great!), the eat up the "solids" that macro algae can't..
Chamber 3 - return, I don't deal with bubble traps or any of that crap. Bubbles are gonig to come from water flowing over the edge of one chamber and dropping (waterfall style) into another, make this chamber big enough and keep your pump to the far side and bubbles usually will not migrate that far, unless it's a HUGE drop.
Alternately you can go a 2 chamber design, instead of a dedicated refugium chamber simply have a combo refugium/return chamber and put some egg crate in there to keep any macro algae from floating into the return pump.
Find where your skimmer exit is, put your carbon there, no need for a dedicated holding area just for that.