In an ideal world, you would have slow flow going into the fuge that then drains via gravity back to the display. This way the pods don't have to go through a return pump to get from the fuge to the tank. That said, I'm not sure it is a common way to do it.
You DO probably want to put your fuge right before the return pump though. I wouldn't want the fuge to feed into the protein skimmer section, as it seems like the protein skimmer would do some damage to any pods that get in there.
The best in sump setup I think is to split your drain line, and have the bulk of the water go to the skimmer section and then return section, and have a lower flow split off the tank drain line and go into a fuge, that then drains into a return section. That would look something like this:
Sump - Model E
Melevsreef.com | Acrylic Sumps & Refugiums
that will allow you to separate and control the flow through the fuge. You don't want it too fast, or you'll wash a lot of the pods away.
If you want to do it in an inline setup, I would go from the tank drain->skimmer section->fuge->return section, so you are not skimming your pods.
Depending on your setup, you might figure out you can't do as much in your sump as you want. I was originally trying to get a fuge in my sump, but just couldn't fit it all.
I ended up adding a fuge on the side of my tank. I split the drain line, it goes to the fuge which then gravity drains into the return chamber. The bulk of the water goes to the skimmer section and then to the return chamber. Kind of like the links above, but I moved the fuge out from the sump.
Benefit of this is you don't have to cram everything into one small place, and you can keep your sump in the dark (keeps the sump WAY WAY cleaner, having no light reaching it.
Here are some pics of my setup
Fuge Plumbing:
Picasa Web Albums - Rob Gillespie
Water into the fuge via gravity (bottom open tube) and 2 drains up top (one is flood protection, haven't used it yet.)
Picasa Web Albums - Rob Gillespie
Front view with macro in the fuge
Picasa Web Albums - Rob Gillespie