Welcome to the Community. I understand that managing bank transactions can be challenging. I'm here to lend a hand to help you address your duplicate entries, @DDOW12.
It looks like your client's online payment went directly into your bank account and was automatically added to your bank register. Meanwhile, you also manually marked the invoice as paid, causing a duplicate payment deposit in QuickBooks.
What we can do here is undo the downloaded payment to bring it back to the Banking page. Then, match it to the manually added payment instead of matching it to the invoice. This will help ensure that the payment is correctly linked to the invoice and avoid the duplication in your bank transactions.
To do this, you can follow these steps:
- Go to the Transactions menu.
- Click the Bank transactions tab and select the bank tile in question.
- Locate the downloaded payment transaction in the Categorized tab that is causing the duplication.
- Select Undo or remove the match for this transaction.
- Then, manually match it to the corresponding invoice payment within QuickBooks.
See this screenshot below for your reference.

Additionally, here's an awesome resource that you can access to have a guide in managing your transactions: Categorize and match online bank transactions in QuickBooks Online.
It's also recommended to perform the reconciliation process regularly to make sure your accounts are matched. To get started, check out this link for the detailed instructions: Learn the reconciliation workflow in QuickBooks.
I'd love to know updates about this. If you have any other questions about managing your bank transactions in QBO, feel free to leave a reply below. I'm just around the corner to help. Have a good one and keep safe.