My own refugium is incorporated with the DSB. Water level above the sand is 250mm deep. Enough to put macro algae in that space. So that means my refugium is a across flow design.
Others options with a dedicated chamber for macro algae can have a bottom inlet and top outlet on the other side, or other way around. Does not really matter. This way you should end up with less settlement at the bottom.
Either options will work, I prefer the DSB combo option, as it provides worms etc also a nice place to stay.