I like to wait a couple of weeks into the cycle and then start it up. It can take up to two weeks for a new skimmer to break in, so two weeks into a cycle should have it fully functional by the time you are ready to add livestock.
I've cycled two tanks and ran the skimmer bother times during the cycle. In my opinion it doesn't affect the cycle or how long it takes to cycle. I think it's beneficial to run the skimmer during a cycle. Plus why not break in the skimmer when the tank is empty? That way it's broken in and ready to skim once you add your livestock.