I always put a sump/skimmer area first, that the water from the display drains into. I then place a couple baffles to help remove microbubbles from the drain water and skimmer. Next is the refugium area, followed by another baffle to help prevent macroalgaes from entering the intake of the return pump. IME it can be difficult preventing the substrate in the refugium from being stirred up if you empty the drain from the display directly into this section (especially if you are moving a large volume of water through your sump). For baffles I just use glass panes siliconed into place. Lowes and home depot will both cut glass to your exact dimensions, and it's quite cheap.
HTH