Auto Pay for a specific time, ie. May Monthly Tuition, and don't include their new balanace of what they've signed up for in the Summer Merged

Parents may pay Quarterly or Monthly Tuition per Quarter. We opened up Summer Sign up in April, and when I went in to charage Monthly Tuition for April or for May, the total included the Summer Balance. I thought the Seasons would be separate esp. when I make the Summer Dates different while using Auto Pay.