How do I add money into a customer's account?

There are two places where you can adjust a user's account. If they have an open order, the easiest place is on the "Edit Order" page for their order. On the left hand side is a section to adjust their account. Give a dollar amount (use a negative number if you're taking money out of their account), type in an explanation of where the money came from (or why you're charging them, if you're taking money out of their account) .If they're paying for orders they have open, check the "apply to open orders" box, and it will add the money to their account and then immediately apply the funds toward their open orders.

If they don't have an order open, you'll see the exact same form on their account details in the "Manage Customers" section.

Either way, the customer will get an email letting them know that you credited (or charged) their account.