Option 1:

To charge a customer's credit card is to click the "Invoices" tab. 

From there you can select which invoices you want to charge on the left-hand side, using the checkboxes.

Then, you click the "Charge CC/ACH On File" dropdown in your Invoice toolbar

Inside the dropdown menu, you can click the "Credit Card" button.

Option 2:

Another way to charge a card is on the "Finances>Payments".

Click the "+Add Payment" button.

Select the customer, invoice, date, and payment amount, then select "Credit Card/Debit Card" as the payment method.

The last step is to click "Add Payment" and select the card to charge.