Step::1 Login to your WHMCS.
Step::2 Hover over the Clients section and click on View/Search clients.
Step::3 Now select the client and go his unpaid invoices and click on the edit icon.
Step::4 On the next page you will get the option to “Remove credit form invoice”.
Step::5 Fill the amount to be deducted and GO.
Step::6 Click on Save Changes.
That's It !
Check out the video tutorial to get in-detailed procedure. Read the blog as well.