Hi there, @olhirons.
Let me help you record these transactions in QuickBooks Online (QBO).
Since the downloaded payment isn't matched to your actual invoices, you'll have to exclude it. Here's how:
- Go to the Banking menu, then select the Banking tab.
- Click the For Review tab.
- Select the checkbox of the transactions to exclude.
- Click Exclude.
Once done, manually record the invoice payment inside QuickBooks. For the overpayment, enter the same amount when receiving the payment. This will create a credit on your customer which you can apply on their next invoices.
If you're not about this process, reach out to your accountant. They can provide you with the right advice in handling your transactions.
For additional reference in applying credits memos, check out this article: How and when to give a credit memo or delayed credit to customers.
Please let me know if you have further questions with regards to this process, olhirons. I'll be here to help. Have a good one!