Personally, I wouldn't put any liverock in the back chamber. The reason why is liverock sheds and by having some sitting back there means it will probably accumilate in there and cause you water quality issues if you can't get down in there to siphon it out regularily. I'd just leave any rock you want to have in your tank in the display area itself where it would be a bit easier for you to manage there. Your display will/should hold enough liverock to biologically filter your tank. If not, then you probably have too much livestock in there LOL. Other than that, maybe run a skimmer and some carbon. I actually ran a skimmer, a bag of carbon and a phosban reactor in the back compartment of my Current USA Aquapod. Not sure how the space looks in the back of the JBJ nano cube, but I was able to squeeze all of that back there along with 3 pumps. When I re-did the backwall (a little DIY I did) I had 5 maxijets sitting in the back of my aquapod (3 for flow, one for the skimmer and one for the phosban reactor) so don't feel like you are too limited just because you have an AIO.
Here are a few pics to show you what I mean.
First setting up. As you can see it's a small compartment but a lot can fit
Another shot before I modded the tank. You can see the skimmer, the bag of carbon clipped on it, the phosban reactor and a fan at the end. The return pump was back there as well.
After modding the tank. 3 maxijets in there for flow and then I put the phosban reactor in there and the skimmer so 5 pumps when it was filled up. Never had any issues with filtration, algae etc. Liverock in the tank did all the biological filtration and the rest of the "filtration" came from the help of skimmer, phosban reactor, carbon and good husbandry.
So...The point is, you can do a lot if you use the right equipment and lay things out properly. This was a smaller AIO than yours. Like I said, not sure what space you hav to work with, but just wanted to give you an idea that eventhough these tanks are small, you can still do a lot with them.
