You can set dynamic shipping rates relevant to the pickup options you have turned on in HK Pickup Options.
Dynamic shipping rates allow you to only show shipping rates to what is relevant to the pickup option chosen by your customer. For example, if a customer chose retail store pickup, they will only see the shipping rate corresponding to retail store, and will not see the shipping rate you have set for pickup at S.F. Express locations.
You can contact our support to facilitate in the process of adding dynamic shipping rates on your store.