Hi
I've got a Reefer 250 and by no means an expert (only just starting out myself) and have the same situation, having done a rumage on the internet it was a bit 50/50 on position of the skimmer, in which chamber etc but it all came back to the benefits of a refugium no matter where it was out weighed not having one and if youre worried about copepods going into the skimmer, it said some would, but nothing to really worry about.