You'll have to create an income account and a service item for your convenience fee. Then, add it as a new line item to your transaction to make it taxable. Let me walk you through how.
Click Accounting, then Chart of Accounts.
Click New. Then, choose "Income" under Account Type.
Choose "Service/Fee Income" under Detail Type. Then, enter a Name.
Click Save and Close.
After that, create a service item following these steps.
Click Gear. Click Products and Services.
Click New, then click Service.
Enter the product/service information and choose the Income Account you created.
Click Save and close.
Once done, add the service item as a new line item to your transaction.
In your invoice, click the convenience fee item.
Enter the Amount, and make sure to mark the Tax column.
Click Save and close.
I've attached some screenshots for you.
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