IMHO using the back of the Biocube 29 as a refugium is pointless. There simply is not enough room back there for any meaningful growth of macro algae to make a dent in nutrient export. The only useful purpose I could find for that space was to host a bunch of marinepure balls as biological media.
In my Biocube the first problem I encountered was the daily need to top up replacement water. Fish can easily go several days without food but you HAVE to be there to top off of or the pump will start sucking air and your salinity will quickly get into the danger zone. So your first purchase should be some sort of auto top off system.
The lights are wimpy, and expensive to upgrade. You can try to retrofit something inside the hood but personally I just took off the top and used a chinese black box LED which was WAY more power than needed but could be turned down. If you like the look of the existing hood you can certainly keep low light things like mushrooms.
I tried 2 different nano sized protein skimmers but both were expensive failures in part because the water level in those back chambers is highly variable without an ATO, so the skimmer did not have a constant water level rendering it useless. That means that water changes will be the main source of nutrient export. If you can commit to 5 gallon water change per week your cube will most likely be successful.
