Usually Amazon fees can be taken into account in the Merchant account. Typically these are the Amazon fees and the subscription charges.
However, if in the month there are not enough sales Amazon charges to credit card. I enter a credit card value of the amount - what else is needed to reconcile this payment etc.
Are you issued with an invoice for the charge at all?
Yes, there is an invoice that shows the amount to be paid and when it will be taken from the credit card.
In that case, you should be able to just create the invoice and tag it as paid from your credit card account
Is it an invoice or is it a purchase from a supplier?
If Amazon are charging you, it would be a purchase invoice. If you are charging someone else, it would be a sales invoice