Hi AegisSCG,

A credit memo is like a negative invoice that lowers a customer's balance. It's also entered if a customer returns an item due to sale cancellation or it's defective. 

On the other hand, when a customer pays in advance or gives you funds to be used on future invoices, the money is entered as an upfront deposit or retainer instead of a credit memo.

Therefore, I would recommend consulting an accounting professional to ask for guidance on how to handle your credit memo because we're unable to use it as a substitute for the credit card payment made by your customer. I can, however, be applied as a payment to future invoices. 

I'm adding this article about creating a credit memo and applying it as a payment to future invoices: Give your customer credit or refund in QuickBooks Desktop for Windows.

Let me know if you have other concerns. I'm just around to help.