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The command slots allow you to select additional commands to run on the station. Each command needs a separate slot, and are mainly used to automate certain areas of the station. This includes things like the Station Manager, Automatic Money Transfer and Automatic Pricing.
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These are the settings used by the station manager (see Station Manager for more info)
Adjust Friend/Foe
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If you prefer, you can hand control over the station to the Station Manager, who will take control of the ships and buy/sell wares where needed. This however costs you wages for the station manager, and reduces the control you have over the station and ships.
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