Allow us to collect easily tuition and then charge those who didn't pay at a later time

We have dancers enroll online and pay tuition early through the system to hold their spot in the class. Then we have dancers on scholarships, who have other family members pay, cannot afford to pre-pay for tuition, etc - these families do not prepary tuition but still have their spot held in the class. When I post tuition for a season, the system does not recognize those who have prepaid and those accounts get charged for tuition twice. This causes a huge headache and a lot of time anulally auditing all accounts one by one. Is there any way to recitify this?