If you have some unpaid invoices or open invoices in QuickBooks Online, then you haven't marked those orders as shipped on Amazon.
Make sure you ship those orders and then mark them as shipped on Amazon. Include any tracking numbers if applicable.
Once Amazon updates the order information, then we'll mark those unpaid invoices as paid.
If you're strictly FBA, then you shouldn't have any open invoices or unpaid balances since Amazon charges when the order is shipped.