Yes! Once you connect your own carrier, any negotiated rates you have with your carrier will automatically appear as the rate in ShipStation.
ShipStation per-shipment fees
Each shipments created using your own carrier accounts (rather than ShipStation's included carriers) will incur an additional fee that will be invoiced to your account monthly. In this case, a "shipment" includes any label, fulfillment, or order marked as shipped. The fee will varies by subscription plan. Go to the Your Carriers Shipment Fees help article for details.
For FedEx accounts with negotiated rates, the rates will appear only after you have created your first label in ShipStation.
For UPS accounts, you must enable negotiated rates in ShipStation first.
Go to Settings > Shipping > Carriers > Your Carriers. Click the action menu and choose Carrier Settings. Check the Enable Negotiated Rates option and enter the requested details from your most recent invoice. Then, click Confirm.
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To enable negotiated rates for UPS, you must have an invoice for that UPS account.
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If you do not yet have an invoice, ShipStation will display the standard rates. However, regardless of the rate displayed by ShipStation, UPS will invoice you at the rate you have agreed upon. Once you receive a UPS invoice, enable negotiated rates in ShipStation and enter your invoice details. ShipStation will then display the negotiated rates.
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If you negotiate new rates for your contract with UPS, you must re-enter your invoice details (follow the steps above) for ShipStation to reflect these new rates.
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For UPS accounts in Australia, add three leading zeroes to the invoice number and use 0000 as the Control ID.