Within the Billing Tools ribbon group, you generate bills for the account you are currently viewing. You can adjust the bill without generating a new bill by either crediting or debiting the account. Once you generate the bill and send it out to the customer, you can apply payments made. Payment made to an account will not show on the account until you generate a bill for the next bill cycle.
Finally, you can rollback a bill cycle. When you perform a rollback, you are deleting the previous bill for the cycle and generating a new bill in its place. Make sure you really want to do this because there is no undo function.