I have a 55 with 10 gal refugium. I run a remora aqua c hang on in the first section of my sump. 2ng section is the refugium, then the last is my pump. I have one of the fatest blue martins around, so a skimmer pulling out pods is not an issue. Everyone that has a refugium still runs a skimmer. Water level.. Not issue once it is running doesn't draw more or less water that is constant. Water noise is no more than that of my pumps which is almost non existent.
Like I said I run skimmer and incoming water into 1st section then a under then over divider to the refugium. Next is the refugium with a under then over divider. Into pump section with some live rock.
Some run pump section in the middle with incoming water and ref. on one side of the pump. On the other side of the pump they have their refugium that gets feed by some of the pump out water via a split off main pump out pipe into the ref.
Hope this helps