Account Number entered in the UPS 3rd Party Billing Account Number and FedEx 3rd Party Billing Account Number fields found by navigating into Setup > Company > Company Information generally applies to all locations when fulfilling a sales order. This serves as a master account for all locations.
To continue charging customers with real time rates based on the account setup under Setup > Accounting > Shipping > Carrier Registration page and at the same time be able to not charge shipping cost on customers with third party billing account, it is recommended to leave the fields for UPS 3rd Party Billing Account Number and FedEx 3rd Party Billing Account Number empty or null.
NetSuite considers an order in determining which account to use in billing shipping charges when Third Party Billing is enabled. See article aboutSet Default a 3rd Party Billing Type in the Item Fulfillment transaction