For anything under $1.00 I either edit the Original Invoice to equal the Payment Received or I receive the Original Invoice amount and let QB enter a Reconciliation Adjustment when I reconcile the Bank Statement.
If you're using the 'Receive Payments' function if there are no other outstanding amounts receivable for the customer the option to either 'Leave this as an underpayment' or to 'write off the extra amount will automatically appear.
If there are other amounts (invoices) receivable from this customer uncheck all of the invoices, and then re-cheque the invoice being paid. The same option should appear.
In case of overpayments the options will be to either 'Leave the credit to be used later' or 'Refund the amount to the customer'