Hello and welcome to the Community, @novaember.

I'm here to help you find the remedy you're looking for. To make sure I understand you correctly, is the Square App importing a duplicate invoice in addition to the one that you create and send directly from QuickBooks? If that's the case, these duplicates will overstate your income. This seems to be in line with the rest of the discussion here, as the option for invoicing with QuickBooks but processing the payment with Square is unavailable at this time.

The suggested method is to invoice and process the payments in Square and then import the sales data, or use QuickBooks for the entire process instead. Everything you could ever need to know about Syncing with Square can be found in our guide at the included link.

While you decide which system works best for you, the instructions below will help you re-assign the payments in the meantime:

1. From QuickBooks Online, navigate to the Sales tab. Select Customers.
2. Click the name of the customer whose invoice you're paying.
3. Click on the Payment to open the transaction.
4. Un-check the invoice that is currently applied to the payment and check the correct one.
5. Click Save and Close.

I'm including a video that displays the process below:

I made certain to reassign a deposited payment to ensure the process works the same way. This will apply the payment to the invoice you created manually in QuickBooks and sent to your customer. Please feel free to get in touch with me here if there's anything else you need. Thanks for reaching out, take care.