I have the same exact question- I was provided a Vendor Credit Memo from the Vendor, after already processing an invoice payment. 

The Vendor then used the credit memo to pay another invoice, which left an open credit. 

The vendor then refunded the difference, however I cannot seem to match this to the credit memo, and when I add it from the Bank transactions, it applies it as a negative number. 

I went in an deducted the amount from the credit memo- and while that brought the balance back to $0.00, it didn't seem like it was the correct way to process the Vendor refund to credit card. 

When I tried to apply the "Bank Deposit" steps to process to this transaction, it did not allow me to select the Credit Card account as the account to deposit the refund into.