If you're setting up an actual refugium and not just a sump, you'll want the skimmer to come after whatever compartment the live rock, macro algea, etc. is in.
If you have the skimmer running off of the drain water, from the tank, it'll pull out alot of nutrients that the macro needs to survive.
You'll want it set up something like this...
It doesnt have to be exactly like that, but you get the idea.