I would run the skimmer and have it help skim out all the extra proteins in the tank. I have always turned my skimmer on the same day my tank was setup. Skimmers do have a break in time where you will have to play with them until they slim up.
This is exactly why I say don't need to. You want those dissolved organics to decompose and get the cycle going... it kind of defeats the purpose if you skim during a cycle.