I partially set up online payment and a customer paid an invoice with a credit card. However, I don't have a bank account linked to QB. Where did the money go?

Let's manually record the payments in QuickBooks, greatgoatslandsc.

After you process a payment, you'll need to record it in QuickBooks to mark the invoice as paid. I'll show you how.

1. Go to + New and then select Receive Payment.
2. Select the name of the customer.
3. From the Payment method drop-down menu, select the payment method.
4. Choose the account you put the payment into. 
5. In the Outstanding Transactions section, select the transaction.
6. When you're done, select Save and New or Save and close.

For more details, please see this article: Record Invoice Payments in QuickBooks Online.

Once done recording, you can now make a bank deposit in QuickBooks Online. This ensures your books are accurate.

Please keep us posted on your progress in recording the transactions. It's my priority to ensure your books are accurate.

Hi greatgoatslandsc,

Hope you’re doing great. I wanted to see how everything about receiving the customer's payment in QuickBooks Online. Do you have any clarifications? If you do, just let me know. I’d be happy to help you at anytime.

Looking forward to your reply. Have a pleasant day ahead!