Nitrates thru the roof

Those numbers are fine for fish. The alkalinity and nitrate might be high enough to cause problems for some corals, but that's not completely clear. I would wait for the Reef Octopus to show up and then give it some time to improve the situation. You might need to do a number of water changes or use some other approach to reduce the phosphate and nitrate levels, because the skimmer can't remove those, although it might allow the other filtration to catch up.

If any animals started having problems, some 15-20% water changes might help. I'd be careful about larger changes. Exposing live rock to air can cause die-off and ammonia spikes.
 
The protein skimmer arrived today. It is installed and running. Water is perfectly clear. I was expecting some yellow or brown i guess , but nothing other than clear water and bubbles.
 
Hmm, it might take some time to get going, or there might be very little organic debris in the water at this point. Hopefully, it can start intercepting some organics before they decay into nitrate and phosphate.
 
What are you thoughts on some nopox dosing now that i have the skimmer up? Is there a cycle time for a skimmer?
 
The issue with new skimmers is the possible presence of mold release agents or something similar on the surface, so it's not actually a cycle time, and it might not happen at all. It's been too long since I bought a new skimmer for me to remember how mine behaved, but I'd give it a bit before expecting much.

You could start the carbon dosing now, but I'd follow a conservative dosing schedule, like the ones in the vodka and vinegar articles, and watch for signs of bacterial slimes or the like.
 
After 10 hours of the skimmer running over night, the cup was half full and the water was a bit yellow. I will test nitrates in a bit to see of there has been any change yet without dosing.
 
A skimmer won't change nitrate levels that quickly. In fact, it won't actually change levels at all. It is there to remove organics before they add to nitrate and phosphate levels. If your nitrates are actually undetectable but you have high phosphate I'd focus on the phosphate. Need to get those two in a balance for the natural processes to work best.
 
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