Apply A Payment To An Invoice

Go to Invoices and then select an Invoice from the Invoice Summary section.

When you receive a non-credit card payment, you can offset the payment against the invoice amount.

To offset a payment amount:  

1. Click the Actions menu icon on the upper right-hand side of the invoice. Then click on Apply Payments. 
2. In the popup window, click the plus icon.
3. Select the Payment Date, and select the Payment Type. The payment type options include cash, check, credit card, or other. Enter the amount paid and optionally enter any notes.
4. Click Add.

The invoice will be updated and display the payments against the amount due.