Question
 

I have heard and read not to use bioballs in the middle compartment of a biocube. what should I use and do in replacements.

bio balls
 

i use small pieces of live rock in mine

Tough question as there are many answers..some people use them and have no problems at all, other people use live rock with great success. All can be potential nitrate factories if you dont watch out..I personally use a wet/dry filter with carbon and just filter sponge..seems to work well for me.

I don't know what the back compartments contain, exactly, or if they already contain these things, but you could run carbon and/or a phosphate remover/binder (rowaphos, phosban, phosar, etc.). I know some others also place live rock rubble in the back compartments, but I would be afraid of detritus build-up, personally.

Could you convert it into a mini refugium? Get some chaeto and a light? Just rambling :)

Drew is giving good advice.

In my nanocube I run phosphate absorbing filter pads in front of the overflow, change them daily because they plug quickly. My hob skimmer pump is in the first chamber, nothing else. Second chamber is phosban, chemipure and carbon. Third chamber contains only the return pump. This seems to be working for me. I'm even starting to win the battle with hair algae.

I haven't had mine running long but I tossed the stock filters 2 months ago and have pulled about half the bioballs out of the centre and put charcoal in there....the rest of the bioballs are soon to go an live rcok will take up that space...Oh ane just added a skimmer to the back right(1st) space.
All my parameters have been great with this (pre -skimmer ) set up

I am running a skimmer in the first compartment and live rock in the second and haven't had any issues thus far. My only complaint is that I bought a 14g instead of the 29g and that is nobody's fault but my own!:lol: