Ok i will try and answer your questions.
Skimmer:
Nutrients in salt water are attracted to the surface tention betwen water and air (i.e. the surface). This is why you often see an oily film on salt water tanks with no skimming. What a skimmer does is replicate the ocean as it hits the coastline. If you watch the coastline you will often see foam where the waves hit the rocks, this is high nutrients and its simply blown away by the wind.
A skimmer works by making a massive amount of micro bubbles appear in a chamber and water is passed through it from the main tank. The nutrients are attracted to the surface area of the bubbles and a foam is formed. The foam rises up and is collected in a cup and simply thrown away. The water which should now be cleaner of nutrients simply passes back into the tank.
Refugium
A Refugium is a 2nd tank "usually" located above the main tank. A pump will push water up to this tank and gravit will allow the water to flow back into the main tank. A refugium is a place where extra filtration such as algae or sand can be kept out of sight of the main system where it doesnt always look as tidy. The most important thing about a refugium however is that its a place for creatures to live and breed without fear of predation from the tanks inhabitants. Copopods and Amphipods are a primary food source for many fish and they soon become deplated in a tank full of liverock as fish are free to pick on them all day long. If you have a refugium then these creature will breed and populte here and the gravity feed to the main tank means that they naturally find their way back to the main tank without fear of damaging them from the impellor blades of a pump. This gives the fish a natural live food source which of course is a good thing. A refugium has many other uses as well of course but its mainy designed to be a "refuge" for something.
RO Water.
Ok Ro water is something many overlook as not being i mportant and regret later on during the setup they have created.
RO water is nutrient free, it is basically free from all additives, chemicals, trace eliments etc. This means you get a pure source of water when you add salt to it. If you add tap water then you carry the danger os any nutrients or chemicals that the water authorities choose to add at any time.
Any nutrients that are in the tap water is food for things like algaes etc..
If you live near farms or agricultured land then you run the risk if having phosphates traces in the water, this is premium food for algaes. And of course, water athorities can without warning add chemicals to kill freshwater rivershrimps that enter their pipes. These chemicals that kill freshwater shrimps is equally fatal to inverts in your tank.
Hope this helps
much appreciated! 
