Hello there, @nbuckler.
You can enter the shipping charge as another line item in the invoice. In the meantime, you'll need to enter a product/service item for the shipping charge and mark it as non-taxable.
I recommend this article for a reference about modifying invoices in QuickBooks: How to Customize Invoices in QuickBooks Online.
If you have any other concerns, please let me know so that I can help. I'm always right here to assist