From an invoice record, it's possible to pay a line item by creating and then applying a payment.
1. Select Records 2. Select Payment 3. Add a New Payment Note: If a deposit already exists, search for the desired deposit and select open (skip to step 6) 4. Add a New Deposit 5. Fill in the appropriate information 6. Once you have created the Deposit select the Payment tab 7. Click on Add Payment 8. Fill in the appropriate information 9. Save and close the Payment and then the Deposit 10. Return to Records > Invoices > open the desired invoice 11. Go to the Payments/Credits tab 12. Note that the payment just created now appears 13. Highlight the payment and select Apply or Auto Apply