If you have items that exceed the limits of USPS or USP (see limits above in How does shipping work for sellers), you can use the Flat Rate option, (the flat rate amounts you set will apply to all your items) or turn off Flat Rate and enable USPS and/or UPS. Then when you enter your weight and dimensions, the item listing form will automatically show a special "Add Shipping Cost" box to enter extra shipping on individual items.
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