You will enter the gross amount of Form 1099K in the income section and then deduct the refunds issued.
But, the steps are a little out of order than what you would expect. When you first set up your business information, you will then proceed to enter the income (1099K would be entered under additional income). You will then be prompted to enter expenses. After entering the expenses, you will have to go back to the Business Summary screen and click "Add Income" (see screenshot). Now, you will see an additional line item for "Rebates/Refunds" (see screenshot) that likely wasn't there the first time through when you entered the income.
