What you’ve done is right, DaoNaturalHealth.
We don't have an option to automatically log in Paypal fees. As long as your Paypal account is connected to QuickBooks, transactions will automatically show within QuickBooks.
There are times transactions look likes appearing twice in the app. Let me share with you why it happened.
Both Paypal and your savings account linked to the app. With that, we’ll see payments as income in your Paypal account, which is the connected one. Once we moved the payments to your bank account, we’ll see it as income again. That’s why we’ll have marked payments as Business Income.
Afterward, transactions from the main account will be marked as a Transfer. You can check out this article for more details about it: Transfers between accounts in QuickBooks Self-Employed.
Let me know if you have other questions or clarifications with this. I'll be here to assist you further. Stay safe and healthy.