Haha, this is a generic "3 chambers" question and definitely not for just nano cube guys.
First off, welcome to saltwater! Jump on in, get your hands wet, then enjoy the dry hand effect it leaves you with later on!
As far as the chambers go, it is all a matter of preference. I believe one thing everyone here can agree on though is that sponges = bad. Sponges do one key thing, collect nitrates, which in a nano tank can turn ugly very fast. A large spike in nitrates = kill off of fish/coral. So definitely remove sponges and bioballs if it came with any.
Now, your back chambers can have a number of things from a skimmer to a media basket depending on how natural you want to go. A skimmer can be a great idea, although far from necessary in a nano tank, but I've typically used one with excellent results on any tank larger then 24G. You can also go with a media basket. If you tank did not come with one already, inTank LLC creates custom ones to fit your back chamber and basically you use the different levels of the basket to put things like macro algea, chemipure, and purigen. All are beneficial additives to a nano. If your center back chamber happens to be a new tank where there is a glass, see through wall, then I would recommend taking advantage of that by creating a small refugium in that center chamber. It is pretty simple in that you get a media basket, let macro grow in it and have a grow light attached to the back. Nano-Glo is an excellent light fro that purpose as it has a magnet that sticks on the inside of the chamber and holds the light on the outside.
So a lot of back chamber setups will be the typical:
Chamber 1: Intank chamber - Typically has a skimmer or is empty
Chamber 2: Center chamber - media basket/macro algae/live rock rubble/purigen/etc.
Chamber 3: Last chamber - Return pump or heater
That's a lot of basic information and like I said, it is all personal preference. This forum is here so you can read up on everyone else's tank's and see what they've done! Good luck and start posting some pictures with your own build thread!