While generating E-invoices, you can also pass the payment details (amount received/due, payment mode) of the invoice.
Let's see how:
Firstly, ensure that you have already recorded the payment details of that particular invoice. (learn how to do that >)
Then, while generating IRN, just click on "Include Payment Details in E-invoice" as shown below: 
As you see above, the details such as Payment Mode, Paid Amount, and Payment Due will be passed to the E-invoicing portal for generating the E-invoice.
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Additional Resources:
How to Generate E-invoices through Refrens? (India)
How to generate E-invoices for SEZ and Export? (India)
How to generate E-invoices for Credit and Debit Notes? (India)
How to Create GSP User Name and Password to Generate E-Invoices on Refrens? (India)
How to show IRN in a single line in documents? (India)
How to view e-invoice acknowledgment no. & date? (India)
How to enable signed QR codes in IRN generated documents? (India)
How to fetch & update E-invoice status of the invoices generated/canceled outside of Refrens? (India)
How to cancel an E-invoice? (India)