If your customer pays you directly after being notified by ItsPayd, you (the merchant) have to manually update the system telling it that your customer has paid. **Please note that this does not apply to users who are connected via API or QuickBooks.
Go to your customers' specific statement which is shown below.
Click "More Actions". When the drop down appears (shown below), click "Enter Payment...".
Enter the total payment, click "Enter Payment".
The following will appear at the top of your Statement Details and you will have successfully marked a payment as resolved.