To charge a guest at checkout or anytime you will need to add the payment to their invoice you need to follow these few simple steps.
First, find the guest you want to add the payment too.
Then, open invoice. Scroll down to find the Add Payment button.
When you click Add Payment the screen below will appear. If you are already integrated with a payment gateway you can select "Use Payment Gateway" and charge the card via the gateway. If you are not integrated then and just want to have a zero balance on the invoice then you can just post the charge and you will not see the payment gateway option.