I have the 29g biocube as well, great great system to start with!
I have my heater in the rear right corner section, its only a 50w so its pretty short and fits just fine. I also have the intank media basket instead of the filter cartridge. It cost like $30 or so and was the best thing I could have bought for my tank. It is three stages and I keep filter padding in the top to catch debris and below that purigen and then on the bottom rack I keep chemipure elite,. The elite has phosphate remover added so it can help big time with algae.
I currently have an open section, I used to have a fuge from intank.com as well but took it out. Defintely ditch the bioballs by the way, useless in my opinion. lol
I am running an in the tank skimmer, an aquaticlife 115 I think it is, cost me like $40 on ebay used and is sooo much better than the stock biocube skimmer and no stones to replace. There is also a slim skim nano that is put out by hydor which is really awesome, but then youre at like $80.
But, if you keep up with weekly water changes you wont really "need" a skimmer, though its nice to have.
Good luck! Let us know what you have in mind for your new project!