I like to run the skimmer the last week of the cycle to break it in. Since you are using one of the bacteria in a bottle products and likely to have a short cycle, I would run it from the start.
I cycled my tank the same way, but i left the skimmer off until one day prior to adding my first fish. I think the instructions states to leave it off for at least 4 hours after dosing.
either way will not hurt. I like to run things during the cycle just like there were livestock in the tank to break stuff in and see if everything is running properly. If it is not running right, I have time to adjust/replace it.
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