I wouldn't run the skimmer during the cycle. It seems many people think the skimmer will make it less stressful on the fish and give them a better chance of surviving, but i think that running a skimmer can cause water quality fluctations down the road. Given that you don't start a new tank off with too many fish, most hardy fish will gain a tolerance to the ammonia and nitrites as they start to rise and will easily survive. A skimmer would just prolong the cycle, and I have even seen spikes in ammonia later after new fish are added.
As Thomas said, I would turn on the skimmer after your first water change, which i recommend to be a week after the nitrites drop down close to zero.