The shipping prices are adjusted on the Account > Shipping page.
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The default options are based on what is available through the different Shipping Services and pings their servers to provide an accurate shipping price based on the weight of the products in the cart. If the weight of the products in the cart exceeds the limit for the shipping option, it will not show up as selectable on the Checkout page.
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To see all the available options, click on the blue service types. For example, clicking Domestic underneath USPS will expand the shipping options available for domestic USPS shipping.
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If you click the Edit link, it will display these options:
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The first option, Per Item Fee, adds in a fee for each item in the cart.
The second option, Per Pound Fee, adds in a fee based on the weight of the products in the cart.
The third option, Fixed Fee, adds that amount every time.
The fourth option, End Price Percentage Fee, is for all the fees, it includes the price gathered from the service itself and gives the customer a percentage of that total.

All these options can be adjusted to create shipping charges that works best for your store.