How will it work at the window? Will the guys on the computer receiving the metal be giving a card with the transaction amount on the card to the customer? Will it be recorded in the books like a check would and the girls will not be involved in the transactions at the window at all?

This is a matter of preference, you could create the payment at the scale if you wish or have the customers go to the cashier window for their receipt. I believe the ATM payments will be accounted for separately in your yard management software, same as cash and checks are separate.