Would it make a difference???

[Lampshade]

It depends on what you want the fuge for. If you're looking for pods for your tank, then running the fuge in parallel to the skimmer may help out more. If you just want the nutrient export then your setup would work great. It may be worth having a bypass on the fuge either way so that you don't have the full flow through there, 400-500gph is what is recommended on a few sites, obviously it'd depend on how big you plan on going.

Sounds pretty cool though, should be a nice setup.