You can either record a prepayment, which is a payment that's made before you've created an invoice for the client. Or you can add a regular payment which is immediately applied to an invoice.
Method 1 - Prepayment
Click the Billing option in the navigation menu and then click the Payments option.
In the sidebar of the payments page, click the Record Payment link.
Complete the details on the form. If you would like to email a payment receipt to the client, then check the "Send Receipt" box.
Click the Save button to record a single payment, or click the Save & Add New button to record more than one payment in succession.
After you've created an invoice for the client, you'll see the prepayment below the Totals section. Click the "Credit this Invoice" link to apply the payment to the invoice.
The allocation form will open. Enter the amount that you want to allocate to the invoice.
Once allocated, the payment will appear below the Total and above the Amount Due line. The Amount Due reflects the remaining balance on the invoice.
Method 2 - Payment Applied to Invoice
A payment form is displayed at the bottom of the invoice page for any invoice that has not been paid in full. This form is pre-filled with the current date and the amount due on the invoice.
Complete the fields on the form including the optional Reference field, the payment method.
To email a receipt to the client check the "Send Receipt" box. You can either click the Save button to record a single payment, or click menu icon to record the payment and immediately go to the next unpaid invoice.
Once the invoice total has been paid, the invoice status will be changed to "Paid".