I don't have a nanocube but I've had a 14 gallon biocube set up for the last year and it's been quite the learning experience.
First off - read as much as you can (which you seem to be doing). I learned as much from what people seem to disagree on as from what everyone agrees on.
Don't rush!! - you know the saying - 'marry in haste, regret at leisure'. Have a plan and try to stick to it. That pretty fish you bought on a whim may terrorize your other tank inhabitants and then hide in your rocks FOREVER. It's also easy to cause a spike when you add too much too quickly in a system as small as a nano. The more bioload you have, the harder it is to keep the system in check and once nuisance algae gets a foothold it's hard to eradicate. - Boy do I know about this one.
I upgraded the return pump in my biocube from the stock pump that it came with and added first a koralia nano mini pump (these are great in nanos, and relatively inexpensive) and then upgraded that to an MP10 when I figured out that the kinds of coral I wanted to keep needed more water movement. After a couple of months, I also upgraded my stock lights.
Like many people, my fans started dying quickly. I replaced them with parts from the manufacturer, but then decided if I was going to have to keep taking the hood off to mess with them that I might as well upgrade to something more reliable, so I got some computer fans online and used those instead - they've been going strong with no more issues for months now.
I also experimented with a few different combinations of carbon, chemipure, purigen, phosban, etc. I've settled on a combination of purigen, chemipure elite and weekly water changes, but your mileage may vary. I don't use a skimmer, but there are a few of them that fit in the back chambers. I'd make sure you need one before devoting precious room to it.
Sometimes I'm a bit stunned by how much crap I've ended up adding to my "all in one", but it was a natural evolution that occurred as I read more and got more specific about the environment I am trying to maintain. I love my nano, but it is true that smaller tanks are harder to keep and require more vigilance.
Good Luck, and keep us updated