Credits DO NOT get automatically applied toward a pay by check balance. Here are the steps to apply a credit toward the balance.
In the side navigation click Team Admin > Lessons Admin.
Click the Acnts/Revenue tab.
Search for the desired account.
Click view in Account Balance column of desired account.
Click [View/Pay/Refund] by desired invoice.
Check the box at the bottom, Check this box to credit -$XX.XX back to this account. As soon as you click it notice it reduces the amount of the check by the amount of the credit.
Enter the Check or reference #.
Click Pay NOW.