Hello usersals,
Welcome to Community! I can understand the benefit of being able to setup and apply late fees automatically in QuickBooks Online. However, this option isn't available at this time. If you would like to see this in future updates, please don't hesitate to submit a suggestion to our Development Team. Customer recommendations are greatly appreciated, in assisting with improving your overall experience with QuickBooks Online.
In the interim, you can add the service fee in your list of products and services, then manually add it as a line item on your forms. Here's a helpful guide, for your reference.
If you have any other questions, feel free to reach out again. We would be glad to help!