I had difficulty applying invoices/vendor credits to the credit card payment.  I believe I have solved it with the assistance of another.  When in our Amex account and there is a payment, I just add the payment.  I then go to the register and look for the payment.  Opening the amount and checking off one invoice from the side box lists all the invoices due plus vendor credits.  Once I start checking it adds up, unfortunately adding the credits does not reduce that total so you have to make sure all the amounts are correct.  I am a bit new to qbo, so it's a learning curve.