I've never really understood having the skimmer before the refugium. If you're growing macroalgae, why not give them a feast instead of just the leftovers? I let my fuge have the "dirtiest" water, and whatever it doesn't use, the skimmer gets.
That said, with 150gph or so moving through my sump, I doubt there's a really significant difference between the water quality in my first and second chamber, so it probably doesn't make too much difference either way. That's my theory on the matter, though.
Of course, another option that seems fairly popular is to split your drain and have half the water go to the fuge while the other half goes to the skimmer. It all meets back up in a third chamber in the middle and gets pumped up to your DT. In short, there are all sorts of ways to do it, and I don't think there's really any one correct answer.