Once the payment has been added, but was not automatically linked to any invoices, you are able to do that manually. 

To link an invoice to a payment, you should open the payment overview. This can be done from Invoicing -> Payments.
From there, you can click on the "Link invoices" button in the "Linked invoices" section of the payment overview.

Now, you are able to search for the invoice by customers name or the invoice number. Once you have found the invoice, simply check the box and click "Add". The invoice has now been linked to this payment!

If you have any further questions, do not hesitate to contact our Support Team from support@insly.com!