Adding a shipping cost allows you to see your shipping margins and set your prices accordingly.

This is a feature that needs to be turned on in the Settings area. To turn on Shipping Markup, just go to Settings > Company > Defaults and select the checkbox under "Shipping Markup."

Now when you go back to the Builder you will see a new "Shipping Cost" field when editing line items.  

Once you have added your shipping costs/prices, you will see the margin reflected in the shipping graph in the Builder and on the Overview page.