If you're importing from eBay, you'll need to enter the shipping costs manually on the "Expenses" tab. eBay unfortunately doesn't include the PayPal shipping costs as part of their automatic import.
In the meantime, the best solution is to do a one-time manual assignment of a category for shipping costs. Sounds hard, but it's actually pretty easy!
You can use the "Other expenses" category or create a custom category such as "Shipping expenses" or "Shipping costs" to track this information. Many eBay sellers do this in lump sums either yearly, monthly or weekly to cut down on manual input.
Now, if you go to a shipping location the Post Office and pay with your business credit or debit card, you'll see a charge show up in GoDaddy Bookkeeping. You only need to classify this as the category you just created ONE time, and from then on every time you visit that Post Office, GoDaddy Bookkeeping will see that you spent money at the Post Office, and automatically put it in your Shipping Expense category.
For your information, any custom category you create will default to be classified under "Other Expenses" for tax purposes, but you can specify whatever tax category you wish under the "Advanced" option. In general, you can leave Shipping Expense underneath "BI" on the Schedule C.
***Note, if you charge more for shipping than it actually costs you to ship an item, the difference will show up as profit.