Mark invoice as paid



I am stumped. We paid an invoice for a trailer (Fixed Asset) with an American Express card. We pay monthly and once the payment comes out of the cash account we download the statement and allocate it to the correct account. I am needing to apply one payment made with the credit card towards an Invoice but it wont let me do it within the  journal entry. 

How would I get around this? Is there a way to associate the invoice with the payment?