I can issue a credit in Customers but cannot apply it in Projects. How do I apply it to get the correct balance?

I'll help you with this, but first, I'll gather information about it, bookkeeper. 

Could you please provide information on the steps you typically follow when applying for credits in projects? Additionally, did you generate an invoice specifically for this project? By providing more information, I can share the correct way to handle this situation properly.
 

In QuickBooks, credits are typically allocated to customers' accounts. The system will create another profile for this particular customer if you create a project (customer name and customer name with the project name you created).  Thus, ensure that you select the correct profile to apply the credits.

Then, I recommend checking this article for tips and additional help about applying credits: Create and apply credit memos or delayed credits in QuickBooks Online.

Afterward, you can follow the steps below to review the total balance (0). 

1. Go to the Sales menu and select the Customers tab.
2. In the Transaction list section, you'll see all the recorded transactions.
   
3. In the Projects section, click the project's name. You'll be routed to the list of transactions under to that project.
   
   

If you're referring to something else, please let me know by commenting below. I'll be right here to provide more details about applying for credits in QuickBooks Online.