Some customers pay small amount like $1 over the invoice amount,so there're credit in their acc. How can i clear it?BTW,it was too less to refund or used in next order.

Your only options to clear are

1. issue refund

2. apply to future purchase

3. Add a new customer inconvenience charge equal to the overpayment. This is now income to you

Your state may have rules on overpayment and treat it as unclaimed funds, meaning tgat one dollar, after a year, has to be sent in to the state. Better to make up a charge and keep the money.