Hi Avinash,
The invoice and debit memo are managed under open item of customer. (you can use report FBL5N to display customer line item to check it).
In order to post amount received from customer, and clear all related open items, you can use tcode F-28 to post incoming payments.
When running this tcode, you fill your customer number, received amount and choose Invoice and debit memo, then save it. The payment document is created and all related open items are cleared.
In this time, when you check report FBL5N again for this customer (choose option all items), you will see the result.
Regards,
Julie