You can use payment tolerance so that every outstanding amount has a set maximum allowed payment tolerance. If the payment tolerance is met, then the payment amount is analyzed as follows:

• If the payment amount is an underpayment, then the outstanding amount is fully closed by the underpayment. A detailed ledger entry is posted to the payment entry so that no remaining amount is left on the applied invoice entry.
  
• If the payment amount is an overpayment, then a new detailed ledger entry is posted to the payment entry so that no remaining amount is left on the payment entry.
  

Reference