Chamber 1 where the water comes in- I run the coral life V2 skimmer (some people also put their heater in this chamber). It's the safest place, as the water level stays consistent.
Chamber two (middle) is where people put their media baskets and yes if you want to run a fuge, this is a common place
Chamber three (where the return pump is) I put seachem purigen at the bottom where the water comes in from chamber two. But i dont think you need that getting started. I also have the coralife UV hooked up here between the return pump and where the water enters the tank. Although, I cant say It makes much a difference and I kind of view it as a glorified lightbulb. Others might disagree with that though, dont don' take my word for it