Algae problem

Video of tank
http://youtu.be/LyDbnr4lapA

I have a 55 gallon reef aquarium with a major algae problem. I have had this problem for a while now. I have a Renu canister filter and a Prism protein skimmer. For a while I was not cleaning the tank like I should have been, but 3 weeks ago I took out most of the rock and scrubbed with a toothbrush to remove excess algae. Since then I have been cleaning protein skimmer 3x a week and doing a weekly water change of 10-20%. I do use tap water from a well, but have used this water for years and have been able to control algae before. I am looking to buy my first ro/di unit (any suggestions would be appreciated). I have had this tank set up for 4 years now. However its only been set up as a reef for a little over a year now. I have a deep sand bed (Fowlr), which lately i have been seeing some lower parts of my sand bed turning black (have read that's decaying matter and sulfate). Please help!! any advice or tips would be greatly appreciated.


Lighting: Current USA 6x54watt t5 (4 months old)

Water parameter:
temp: 80.0F
Nitrate: 0
Phosphate: 0
Ammonia: 0
Calcium: 325 (low working on raising
Kh: 250 (high working on lowering a bit)

Fish/inverts
1 lemon peel angel
1 tomato clown
2 damsels
1 blue sea star
1 coral branded shrimp
red hermit crabs and shrimp (not sure on exact number anymore)

Coral
hammer coral
green flower pot gonipora
leather toadstool.

My lights run for 12 hours. How long should I be running my lights for?

Powerheads are working. I have three of them in the tank. The canister filter I have been cleaning once a week (for the last three weeks). However before I that it was probably once a month. I have been changing the carbon more frequently as well.

I have heard that even though nitrates and phosphates are reading zero that some times when you have a lot of algae they can absorb it faster than my test would be able to detect it. Is this true

Only feeding the fish every other day. I also spot feed the corals 2x week. So I don't think overfeeding is an issue. I have tested freshly mixed saltwater and nitrates and phosphates are zero.

I do have an older deep sand bed, Is it possible for the sandbed to be leaching somehting out that the algae is feeding on? I have been debating whether to remove some of it. I am starting to see quite a lot of black sand and have been trying to research it and have found mixed feelings on it.

I actually just started buying the Chemipure bags for the canister (3 months ago). I don't think they were elite though. I will defiantly be looking into those