Hello there, @psanzi.
You'll be happy to know that you can consider entering a credit card number in the reference section. And I'd be glad to share some information about this.
When entering a reference number on the sales receipt, it's better to use the check number if they paid it by check and the last 4 digits of the Credit Card if they paid via credit card. This way, you can easily locate the transaction by their reference number.
You can also check out this article for further guidance about Sales Receipts: Sales Receipts in QuickBooks.
Fill me in if you have further questions about Sales Receipt. I'll be around if you need any help.