To apply security deposits you would go to the Billing tab > Overview. From here, you will select the parent(s) that you wish to apply security deposits to by selecting the check boxes by their name(s). Then you will need to click on the top drop down menu and select Apply Security Deposits. You will be brought to a screen where you will apply the credits or security deposits. To apply, click the check box under Apply and it will apply it to the latest outstanding invoice. You will do this for all parents in the list. Click Save & Close when you are done.
If you wish to apply a security deposit for one payer, you would go to their billing > click the down arrow in the payer's billing account > click the drop down menu > select Apply Security Deposit. To apply, click the check box under Apply and it will apply it to the latest outstanding invoice. Click Save & Close when you are done.