Hi MrMiyagi,

To be able to apply the Journal entry to the invoice, use the Receive payment option in QuickBooks Online. Here's how:

1. Click on the Sales tab.
2. Click on All Sales, locate the invoice.
3. Click on Receive Payment on the invoice you wanted to apply the journal entry.
4. Under Outstanding Transactions, tick box for invoice and under Credits tick box on the Journal entry.
5. Click on Save and new or Save and close.

You can check this link to learn more about how to Apply a journal entry credit to an invoice in QuickBooks Online.

Let me know if you need more information with QuickBooks Online. I'm always here to help. Have a great rest of the day!