I have a remote 'fuge that gravity feeds into my display tank. My goal is to sustain a huge amount of 'pods without the fear of them being killed by pumps, skimmer, etc. A skimmer will remove the occasional pod or two, but unless they are in very short supply, I don't see why a skimmer killing a few pods would outweigh its benefits to a tank. If you are seriously worried for your pods, then I would look at encouraging them to multiply in the tank in large numbers, perhaps with a pile of live rock rubble in an area of low flow seeded with some pods and an occasional pinch of food to keep them happy and multiplying.
-Joe