So with credit invoices there are two ways of handling the reconciliation in QuickBooks. 

Customer pays direct into bank account (BACS, Bank Transfer, etc.)

If the customer pays directly into your bank account (BACS, Bank Transfer, etc.) then the money will appear in your bank feed and can be reconciled to the invoice or multiple invoices that the payment relates to
 

Customer pays at trade counter (Cash, Card, Cheque, etc.)

If the customer comes into the trade counter, whoever is serving can take an account payment for the customer.  Ideally they select the invoice(s) that the payment relates to (in Customer record > Financials tab) and then take the card/cash/cheque payment for that amount into the cash drawer, like a cash sale.  

This will then show the account payment on the End of Day report, along with the cash sales.  It will also have a text reference to the invoices the customer wanted to pay off.  When the money from the cash drawer is banked, and appears from the bank in QuickBooks, you can match off the money against the cash sales and the credit invoices that are being paid off.