no matter where the skimmer is, it's not going to take everything out of the water before it passes. you could have it hanging on the tank, in the sump, or completely external and it (and the refugium) will still work. you are giving the skimmer too much credit.
think of this- if the skimmer worked that well, why would we even need macros?
as for flow, i would look into vortechs if you want a clean DT (display tank), but you aren't going to be able to achieve adequate flow with a return pump. you are better off saving that pump for use in a closed loop, and buy something smaller for the return. maybe even return that pump and get something larger for a CL
. i used a reeflo barracuda (4300gph) for my 195 gallon DT.