Hi there, @AegisSCG.
Thanks for getting back and providing additional information about your concern.
When using QuickBooks Payments, the invoices are marked as paid after your customers send the payment. In your situation, since you recorded payment via Receive payment feature, you'll need to delete it to resolve duplicate.
Then, if the payments are by default deposited to the Undeposited funds in QuickBooks Online (QBO), you'll need to create a bank deposit that includes the processing fee. To check your settings, here's how:
- Go to the Gear icon at the top.
- Select Account and Settings.
- Choose the Payments tab.
- Go to the Chart of Accounts section.
- Review where the payments and fees are deposited.
- Click Save and Done.
Once done, you can match it to the Banking page once the payments are cleared from your bank.
In case you want to review your transactions after matching them, here's a resource that you can visit: Find, Review, and Edit Transactions in your Account Register.
As for your other concern, the option to directly move your data from QBO to QuickBooks Desktop (QBDT) is exporting and then converting your QBO data to QBDT. Just a heads up, things will look different after the process. You can click this link for more details about the limitations when you convert: Learn how features and data move from QuickBooks Online to QuickBooks Desktop.
For your future reference, you may consider reading this article to guide you in reviewing your accounts to make sure they match your real-life bank statements: Reconcile an account in QuickBooks Online
If there's anything else I can help you with, please let me know. I'll be around to help. Have a great rest of your day!
