I also have a live sand bed about 4-5 inches deep. The top is nice and white, but the underlying sand layer is dark grey. That is normal and you dont want to disturb more than the upper inch of your sand as the lower layer is where all your denitrification is taking place. That said, you do need to put in some extra effort withthe sand beds. They tend to 'stagnate' and you cant really vacuum them, so you need to rely on God's creatures to helpyou out. Sand sifting critters like Nassarius snails, a cucumber, a good sandsifting gobie all help tremendously. When you do your water changes(I do 20% every other week), stir up the top layer of the sand only. I use my hand and a very fine net to remove anything that may be sitting on the top of the sand. You also need to make sure you have adequate aeration in the bottom of your tank. Place a submersible pump a couple of inches off the bottom so that it does not blow the sand around, but moves the water just above it.
As far as the brown stuff, it is Cyano-and is tough to get rid of, but you can if you are consitant in
significant water changes with ro/di water.
not overfeeding,
having the proper creatures in your tank to keep sand stirred up
adequate filtration and aeration.
The Cyano can be peeled off the sand if it gets too thick. Do NOT let it get on your live rock even if you have to take a toothbrush to the rock and get it off. If bad enough, this stuff will cover your corals, and anything else in your tank.
If you keep after it, you will livk the problem in about 5-6 weeks. You may also find it helpful to add some PHosphate removing pads to your filter system. I keep these in my sump drawer and change them weekly since I did have a Cyano problem at one time.
Good Luck-Dont give up.
