John - your orignial question regarding phosphate and nitrates are simple enough. Do a water change? This is the simplest thing you can do to help remove the PO4 and NO3's at this point if they are as high as you think they are, and at this point if they are really bad do up to a 50% water change. As long as you have an established tank it should recover just fine. Adding a phosphate remover at this point would take to long. So the water change is your best fastest bet. USE RO/DI WATER.
With regards to the growth of coralline algea you will need to keep your Calcium at 400 -450, and Alk of 10 -14 DKH, mag 1300 -1500. This is also where the water change will help replenish natural buffers and keep the system in balance. You will probably want a two part buffering system like B-Ionic to add after you get things balanced.
With the substrate that you have, you seem to have the reverse crushed coral and sand with CC on the bottom and sand on top. The CC will eventually work its way back on top, law of nature. With CC on the bottom you will have problems: It is my thought that with the CC on bottom you will not be able to build any anoxic areas that will be able to proccess the nitrates and waste, therefore once the detrus gets underneath the sand it is traped in the crushed coral and it becomes a nutrient sink that will pollute your tank.
If it were me I would only have one or the other of substrates, I would not combine the two. CC you can vaccum and maintain. Sand you only have to keep waterflow high to carry the detrus in suspension in order to have the protien skimmer remove it + the wet/dry or other machanical filtration.
Does that help?
Thomas