Once the applicant applies for a permit on the kiosk and hits Pay at Counter, the application is submitted and on the Process Orders list.  To confirm that the applicant has paid the cash due, click on the Payment Received link under the Order Status

A confirm payment pop-up window will appear where you can enter any notes, e.g. the check number if you accept checks.

Once you hit Paid, the application will open and be assigned to the user who confirmed the payment.  The system will also track the who confirmed the payment and when it was confirmed.