How to pay invoice from customer balance

Scenario:
Customer makes a payment, ledger adds funds to bank and credits debtors. This can be seen as a customer credit balance.
An invoice is created later, but user fails to allocate a prepayment. The invoice gets submitted. How do I make a payment for this invoice to use the customer’s credit balance?

Is there a special Payment Entry Type to create with a specific account?

You can just reconcile the advance payment with the invoice using Payment Reconciliation if you have the advance payments feature turned on.

https://docs.frappe.io/erpnext/user/manual/en/advance-in-separate-party-account