Glad to have you here on the Community page, @KungFuMel.

You're right in converting 50% of the estimate into an invoice. Once a percentage or an amount is added to an invoice, it'll display a current balance under the Customer section.

You can apply the remaining balance by recording a new invoice, then add the amounts of the estimate. I can guide you on how.

1. Select Create Invoices from the Customer tab.
2. Pick the customer's name beside the Customer:Job section.
3. Add the remaining amount of the estimate.
4. Save the transaction.

To learn more about estimates, you can check out this link: Create an estimate in QuickBooks Desktop.

Also, here's an article you can read more about the AR workflows in QuickBooks Desktop: Get started with customer transaction workflows in QuickBooks Desktop.

If you have any other questions, please feel free to leave a comment below. I'm more than happy to help. Wishing you a happy holiday!