I would always put them prior to the refugium. Cheato, detritus,and other things that may make their way through are good at clogging pumps and/or the media. Sure you can use prefilters on each one (and what I would generally do anyway), but why make it so they clog and need cleaned/replaced more frequently when you can just have any reactors prior to the refugium and make it less of a concern.
As for pods depending on the pods you are talking about many will be large enough to get stuck in mechanical filtration and some types of media like gfo. Its not the end of the world, but again if the goal is maximizing their population then no reason to not put that stuff upstream of the refugium.