The typical recommendation is to bill the project for the full value of the work. Create a credit memo to apply against it. And lastly, send the client the invoice so that they can see the value of the work being done at no charge.
The credit memo would either go against the original sales account on the positive client invoice or if you set up a Charity income account and post to that account, which will make that account go negative. So when they look at their sales account balances, they would see the positive income going to agency fees, for example, and then a negative amount going to a Charity income account.
This is called a "contra-income" account. "contra" simply means that it'll hold a balance that is negative instead of positive.