It's been a while since I did this, but I believe you should look at overriding the SendEmailNotificationInternal() method by implementing a custom OrderInfoProvider class. This method gets passed in the ShoppingCart object which is used to get the CustomerInfo and thereby the email address.
I do believe there are several SendOrderXXXXNotification() methods and you may be able to override just the payment notification, but by default Kentico internally just feeds these through to the SendEmailNotification() method.