In the POS application you can record an invoice payment. Just go to the Bill history section and in the bottom left corner select the red Pay invoice button.
A form will appear where you need to fill in the amount of the paid invoice and the invoice number (which you can find on the invoice issued from your accounting system). You can enter the receipt sequence number or choose a digital confirmation (the payment confirmation will be sent by email). You can also select the payment method that was used to pay the invoice.
After filling in the details, just click Confirm and, if the Digital option is not ticked, a confirmation of the invoice payment will be printed.