I've got the biocube 29 also. Only had it about a month. I also purchased the biocube skimmer.
The instructions do suck. I talked to the people at my lfs and they said to take the filter out and hang the unit on the plastic divider between chamber 1 and 2. And to take the filter and lay it above the bioball cover so that the water flows over the filter material. I plan on getting other filter media to do the job once I use up the filters I bought with the cube. I also am able to fit my heater in the same chamber as the skimmer.
I set up the skimmer when I added my live rock and it's worked like a charm. I had to adjust it a couple of times to get it set right. Take the top collection chamber off and turn up the airflow. You want the bubbles to just start to get to the top of the tube. They may not even break over the edge, but once it has run for awhile with the collection chamber attached, you will get an accumulation of gunk. If you have RO water and salt only in the tank, it will not work as well. Nothing to cook out.
I realize that this is not by a long shot the best skimmer around, but it fits my tank and it works just fine for me. You just have to change the airstone monthly.