biocube has 3 chambers in the back. take the bioballs out and replace with live rock rubble or some sort of media. 2 jars of seachem media is what i used. then place some carbon bags over top of the rubble. and now place the polyfilter on top of everything and i still use the plastic crate to diperse water all over the poly.
you can buy an oceanic protein skimmer made for the biocube 14 / 29 gallon. not the best but does a decent job for 50 bucks.
good luck.
As far as a refugium i have seen it done but i have no experience with that but definately google it. and check other forums.
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29 g biocube /25 lbs LR/ 20 lbs LS/ 1 oceanic protein skimmer
Filter In Middle Chamber: sponge+Seachem Matrix biofiltration media+2 bags of activated carbon
10,000k power compact/actinic pc/3 moonlightLED
fish: potters angel / sixline wrasse / yellowheadsleeper goby / bicolor blenny /
inverts: fire shrimp / blue leg hermits / scarlet hermits / snails / conch. | 
