By default, invoice payments are meant to be paid separately and directly by clients. However, at any point after creating an invoice, you can offset the invoice amount by way of direct payment or balances available in the trust or operating account.
To add payments on an invoice:
1. Head over to Invoices
2. Hover on a choiced invoice and click Record Payment in the pop-up menu
3. Select any Payment Source
4. Choose Source
5. Select the Destination account
6. Click Add Payment