First step to charging autocharges is to record your customers credit card information inside of CLIPitc.
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You can do this from the customer account page.

Or Single payment page. After processing an amount (or a 0.00 charge) then on the next screen you can check the Save card for autopay option.

A third way to get the autopay information into the program would be to ask your customers to enter the information into the Customer portal section.

After the customer's card is entered and selected for autopay you can charge them in the Invoice>Process Autopays section.

Click on Invoice, then click on "Process Auto Pays".
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Next you will see a list of customers that have an outstanding balance, and have the autopay option selected. Check the customers that you want to charge, or check the box at the top to charge all customers. Once the customers that you want to charge are selected click on the "Process" button.

To view previous batches of autopays you can click on the "View Past Batches" button.

To view the individual transactions click on the "View Details" link.
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You can see the details for the transaction including the status, and last 4 digits of the cards.
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That's it. You can run autopay's as often as necessary. Typically you would invoice for the month, then run the autopay's after the invoices have been reviewed.