Skimmer water fudge mmmmmmm.....
Is it a seperate refugium or in your sump?
Is it the only water flow to the fuge?
Try to have your skimmer upstream from your fuge to get the raw water from your tank then I don't think it matters if the skimmer discharges into the fuge. It might help with bubbles depending on how your setup.
My skimmers are at the return end of my sump, which isn't the greatest and they discharge back into a sock in the refugium.