Option 1 (Most accurate for the Vendor record) 
- Replace the original invoice with a new invoice for the new/corrected amount. 
1. Open the Invoice record
2. Note all applicable information
3. Delete the invoice
4. Re-create the invoice with the correct amount (less the credit)

OR

Option 2 (via the Bank)
- Leave the invoice for the full amount of the item and then create a bank adjustment to the credit card register. 
1. In Banks > Open the Credit Card bank
2. Open Register > Click New Adjustment at the top
3. Select or create a new category for Payment
4. Enter Date, Amount and select a type of Payment
5. Add a reference, GL distribution and a post date
6. Save and close the adjustment


Full example: You paid $1000 to Office depot using your Visa and have a $200 store credit:

1)    Re-enter the invoice for the net amount ($800) yielding the following accounting entry and accurately tracking vendor spend

Office Supplies Exp           $800
              CC Liability acct                $800

Visa Register
TypePayments/CreditsCharges
Credit Card Charge $800

            
OR

2)    Leave/Enter the invoice for $1000 and a bank adjustment of $200 (your accounting will be right and you will see the $200 in your Visa register, but your vendor spend will be wrong (bc the $200 adjustment is NOT tied to a vendor)


Office Supplies Exp           $1000
            CC Liability acct                $1000

CC Liability acct                $200
           Store credit/Office Supplies Exp   $200


Visa Register
TypePayments/CreditsCharges
Credit Card Charge $800
Adjustment$200