If the difference is small, adjust the difference between the invoiced amount and that actual payment amount by using the adjustment option under the reconciliation tab.
If the difference is big, add a new transaction my using the find and match function. Click on the find and match tab and use the find and match function to match the invoice. Then click on new transaction and then receive money. Enter in the necessary details such as the date it was received, and the difference between the invoice and payment to match the invoice and payment.