Let me provide clarifications regarding this payment concern, @Ptonjalken.

You'll need to change the account of the deposit from checking to A/R. This way, you'll be able to receive the payment and link it to the open invoice.

To change the account of the deposit, just look for the transaction on the register. Then change the Payee Account to A/R and Save it afterward. Please see the sample snip attached for your reference:

After that, you can now receive the payment and link it to the open invoice. 

Here's how:

1. From the Plus (+) icon, select Receive payment under Customers.
2. Select the customer's name under the Customer section.
3. Look for the invoice you want to pay under the Outstanding Transactions section.
4. Select the Deposit recorded under the Credits section to apply it to the invoice.
5. Tap Save and close to record the transaction. 

To give you the complete process of receiving payments in QBO, please see this link: Learn how to receive and record the accounting for invoice payments.

However, if you're unable to change the account, I'd like to ask for a screenshot of your setup. This can help me to picture out this matter and provide an accurate resolution.

Please get back to me on how things turn out. I'll make sure you're all set. Keep safe!