Thanks for posting in the Community, alex90.

You can only select a payment method once you receive payment for an invoice. Let me walk you through the steps:

1. Click the Sales tab on the left menu.
2. Go to the Invoices tab.
3. Select the invoice.
4. Under Actions, click Receive payment to pay an invoice.
5. Click the drop-down arrow under the Payment method field.
   
6. Check the invoice number that you want to pay.
7. Click Save and close.

For future reference, you can reconcile your account to match your credit card and bank statements. Please visit this article: Reconcile An Account In QuickBooks Online.

You can touch base if you need further assistance.