Yes, there's a way to automatically apply payments to an invoice in QuickBooks Online (QBO), iamgavinjones.

Thank you for the screenshot. You don't need to create a rule for the deposit to automatically apply to the invoice.

QBO has an automation feature where you can automatically apply payments to an open invoice. This option can be turned on in the Account and Settings section.

Here's how:
 

1. Go to the Gear icon.
2. Choose Account and Settings.
3. Select Advanced on the left of the screen.
4. Click the Pencil icon in Automation.
5. Mark the Automatically apply credits box.
   
6. Click Save, then Done.

If these payments are creating an overpayment, I recommend the following article which contains steps for what to do: Apply A Credit From An Overpayment.

QuickBooks estimates and invoices are improving. Check out this link to learn about the latest update: See what’s new with estimates and invoices in QuickBooks Online. The workflow for these forms will look different depending on whether you have the old or the new version of estimates and invoices.
 

Let me know if you have other concerns aside from applying payments to invoices. I'll be right here to help you.