You may need to charge a customer directly through Stripe or Braintree. If you are using Braintree, please visit this link. The rest of this guide will be for Stripe only.
Log in to Stripe.
Search for the customer.
Scroll down to the Payments section and click the + Create Payment button.
Enter the currency, amount and be sure to note in the description that it's a manual charge. This will help you in the future when you need to quickly know the reason for this.