I think most people run their Chemical filtration, like GFO/Carbon, Biopellets, after their refugiums not before... That way, like Ian said, the macros in the fuge get the most nutrient update possible and the chemical filtering is an after process cleaning up the leftover...
I run a 3 chamber sump. 1st = Skimmer, no filter socks. 2nd = 6" DSB, rubble, and Chaeto on top, 3rd = BioPellets with return to 1st chamber for bacteria skimming afterwards, GFO/Carbon with return back to 3rd and then finally return pump back to DT. I run the BioPellets and GFO/Carbon last so mechanical filtering has already happened in 1st and 2nd chambers, so the media filters don't get clogged as easily...