If you update a team's status with a league (for example you change their status from "Interest" to "Fully paid") because you have taken a payment from that team, you must ALSO add a payment for that team via their statement. If you do not add a payment for the team, their statement will still show an outstanding amount.
To add a payment, view the statement for the team in question, and then click "Add a payment for this team". Select a payment type other than "Credit card" if you have already accepted payment - payment types of "Credit card" will take you to the payment gateway.