Once Payments have been setup, they can be applied to Invoices when payment has been received.

Open the invoice detail page of the invoice you want to apply a payment to and click on the Add Payment button.  Choose the Amount and Payment Method and click Submit.

The payment will then display on the invoice.    If there are multiple payment types, repeat the process until the payment balance matches what has been paid.  

You can then use the relevant document template fields to display the payment type and amount and the total due as required on your invoice templates.