Hello there, streetortrack.
There are many applications that you can integrate with QuickBooks Desktop to manage those payment.
You can check out this link to see if your third-party application is compatible with QuickBooks Desktop: Apps for QuickBooks Desktop.
If you don't see the app you're using, I suggest contacting the third-party app support to help you import those transactions to QuickBooks.
I've also added this article to learn more about importing data to QuickBooks desktop.
Let me know if you still have other questions about payments. I'll keep an eye on your response. Have a good day!