Your rock and sand will take care of it while cycling. When it comes to the skimmer, it takes several weeks for it to "tune in" and work correctly. It isn't necessary to tune it in during the cycle, as it can go wonky and possibly overflow the cup quickly. This would be bad if you are running a HOB
skimmer. I would just cycle the tank and then hook the skimmer up and let it tune in while you slowly begin adding livestock upon completion of the cycle.
While cycling, the only things that matter are ammonia, nitrites, and nitrates. Anything else just complicates things and I am a firm believer in the KISS effect.