A customer can pay before you send an invoice, or pay the same invoice two times. You can match this payment to the customer with no invoice. The full amount stays as unapplied credit on the customer's account.
Match the payment to a customer
In Reconciliation, select the bank transaction. Do not select an invoice.
In Pre-payment / Overpayment, click Add a new line.
Select the customer. Enter the full amount of the bank transaction, with no commas (for example, 1000.00).
Click Match. In the Match plan, click Match again.
Reconcile the match on the Review & reconcile tab.
The bank transaction must be money in, and the full amount must go to one customer. If Match stays disabled, put your pointer on it to see the reason.