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For your website shopping cart, the time at which the customer's credit card gets charged depends on the Checkout Method you are using. If you log into your site and look under the Admin button with your username in the upper right, click on Settings > Website Settings > Products.

The default checkout method is Sale, and the way that works is that when the customer checks out, their card is charged right then, and you are notified about the order. In this method you cannot change the final amount, but you can contact the customer if you need to charge them more for shipping or you can give them a refund if you don't have everything they ordered.

The other method is Authorization. At the point of checkout, this method does not charge the customer's card right away, but it does authorize the funds. The customer receives an email letting them know their order has been pre-authorized and that they will receive a receipt as soon as the order has been processed. They do not see a final amount at this point. You are able to go into your PayPal account and you can alter the final amount as needed to fit shipping costs and or altered quantity amounts. If the order wasn't processed by PayPal, you can go into your Orders module and click to View the order and work with shipping, fulfillment status, and possible refunds or voids from there. You can also contact the customer if needed. You then click a Capture Funds button and that is when their card is charged and they are sent a receipt.

The advantage of using Authorization is that you have the ability to adjust the amount to be charged as needed before the charge goes through, reducing your refunds.