Ok, you want to set up your sump for macroalgae most likely. Your Local Fish Store (LFS) might have some that they can sell you by the bag. But you want water to come from the tank, flow over one wall, into the chamber with macroalgae and usually a deeper sand bed in it. This will pull out a good deal of chemicals that you DO NOT want in your tank. Then it should flow into a third chamber where the protein skimmer is (unless it hangs on the tank) and be pumped back to the tank. YOU DO NOT want sand and macroalgae getting into the first or last chamber, ONLY the middle one. This should take about a day to set up. Then, I have never heard of an Aqua Reef protein skimmer, do you mean AquaC protein skimmer? If so, you want that running too.
Keep in mind that if you are going to want to add clams or tunicates or anything that dissolve filter feeds off of nitrates and phosphates or ammonia, you will probably want to allow a LITTLE bit to get in to your system for them to survive off of. Looking at those brown spots a bit closer, they look like Diatoms almost. Look for picture of Diatoms on the net and try to compare pictures. If it is Diatoms, this usually means that you are coming to the end of your cycle. You just need something to take care of that extra bit of nitrates that are in your tank and you should be good. AND PLEASE keep your tank out of any area where sunlight can hit it.
The sump should look sort of like this [A]___B___[C] A. First chamber where water comes from the tank, water flows over that wall into B the second chamber, that is where the macroalgae and deeper sand bed is and then over the wall into C, the third chamber where the skimmer is and where it gets returned to the tank. I just have no idea what kind of skimmer you have so am going off of what MIGHT work. You can cut grooves in plastic if it isn't already there or use Nylon screen to seperate the chambers usually.
If you are going to purchase corals though, please try to make sure that you have the test kits and additives around to maintain their health. Salifert makes really good calcium and alkalinity test kist (at least I have had really good luck with them) and you want to make sure that you maintain your calcium and alkalinity where it should be.
