hey Silver,
I have a 29 gal Biocube. I am running the proprietary Biocube protein skimmer as well. What you will have to do is remove the filter cartridge in chamber one and hang the skimmer on the dividing wall between chambers one and two. if you do this, you will be able to fit a heater in chamber one along with the skimmer. I have a Stealth 100w in there. you will have to knock out the false bottom to do so though because the heater is too long. Its not that hard to do, just get a long blunt object and slowly apply downforce until it goes.
Because i removed the filter cartridge, I bought an Aqua-Pure filter media bag from petsmart and filled it with carbon and laid it on top of the bio balls then i cut some filter floss to size and placed it over the carbon sock and then topped it off with the stock grate that covers chamber two.
I had the same dilemma when i first bought the skimmer. not sure why oceanic didnt make the skimmer to accomodate the use of the stock filter cartridge. they dont make it clear in the instructions of where to put the skimmer either. i think the original design for the biocube was to have the filter cartridge flush up against the intake in chamber one where the water intakes are and thats when they designed the skimmer because that seems like it would actually make sense and everything would fit.
Good luck!!
