First off your system is 2 months old and still cycling and yes you nutrient levels and going to be all over the place. I also would not advise running bio pellets with AF systems, from my experience of running bio pellets is was not good.
I would suggest
running GFO, carbon and the life bio fil media, this will help with controling your nutrients.
I would suggest also running AF 1+2+3+ for you systems parameters and elements along with reef salt. You can also dose ABE&V and that is all you would need if you feed the mysis plus some other fine food with our frozen.
Run Phosphate at .02 to .04 is a good thing for a reef thank and nitrates of 3 to 12 or higher depending how your system looks. At this point you are more concerned with the phosphates. If you need to get your phosphates in line pretty quick I would suggest looking at products that use lanthanum chloride
link.