Spiral,
Okay I talked with several people and they had the same answer. You will get your source / intake water from the prefilter side of the system to supply the refugium. So from the below picture on my tank it is the far right side just before the white filter pad. You will then pump the water from the the refugium back to the far left side of the system which will then be pumped into the main tank.
The other option I was given was to remove the bio balls and turn that into the refugium. I have not decided as to which way i am going to go.
I hope this makes sense. I am going to work on mine as soon as I can. I just got my tank today so I have alot of other work to do.