You can make partial payments to invoices online.
Enable Partial Payments must be switched on in your Settings.
Go to Control Panel > Settings
Click the toggle Enable Partial Payments.
Click Save Settings.
Search for the invoice under the Invoices tab to pull up the invoice.
Click on Pay Invoice. From here, you can add a stored card and then pay with the stored card, or create a transaction.
On the payment screen under Order Information, edit the payment amount to the amount desired.
The invoice will automatically be updated to show the new amount due in Biller Genie, and will sync back to your accounting software.