I have ran it both ways and I personally prefer running the skimmer before the fuge. Whether it's true or not, I like to think of it as the fuge is "refreshing" the water right before it goes back into the tank. I would rather put as much nutrients back into my water as possible. Let the skimmer do its job and skim out all the gunk, but then allow the water a chance to carry any beneficial nutrients it can pick up running thru the fuge before it goes back to your tank.
My fuge contains LR rubble, miracle mud, 4 different types of macroalgae, and pods. Not alot of folks like the miracle mud, but I really see the benefit when I have used it to when I haven't.
Whichever you way you go, do what you feel is best for you. You may want to try and put in a larger sump if you can (the bigger the better), there are some nice ATO reservoir's out there that can fit nicely and look pleasing to the eye next to your tank/cabinet to help you free up space inside of it so you can fit a larger sump.
Keep us posted and post lots of pics!
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