When creating a payment, if a value greater than the outstanding balance is entered, then the invoice will be marked as fully paid as shown in Figure 5 and an "over-payment" will be created as shown in Figure 6.
To view all payments for a Sales Order, look at the top right corner of your screen:
After creation, over-payments act identically to credit notes. They represent a credit to the customer's account and their value can be applied to future invoices.
After creating an over-payment, if you wish to undo the whole operation, you'll need to delete both the invoice payment and the over-payment from the sale.
You can also create a Refund as shown in Figure 7 below:
You can also see what is "outstanding" at a higher level (for all sales orders) by selecting Invoices from your left main menu or looking at your dashboard.