In order to apply client credit, create a new Change Order for a negative amount. That can be done in the Contract & Change Orders section:
Scroll down the contract and click to add a new change order:
Fill out the information in the provided boxes below. Enter a negative value for the change order amount, and click Make Active to add immediately, or Send Out for Signature to receive approval from the client:
Once this negative change order is added, we will invoice the total amount. Invoicing can be found at the top-right part of the screen.
When beginning the invoice, enter credit percentage you would like to apply. As a shortcut, you can click the arrow (highlighted in green) to change the corresponding completion percentage to 100%. Click Confirm to continue:
After reviewing the invoice, click Verify and Finalize to populate the invoice summary. As noted below, this negative invoice will not be sent over to QuickBooks. Finalizing this invoice will affect Knowify’s numbers only. Click Finalize to continue: 
After this invoice is completed, create a matching negative invoice in QuickBooks. This will catch up QuickBooks to the most recent Knowify data.