Can parents enroll one student in AutoPay and not another?

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AutoPay is invoiced based, so this depends on what level your school is invoicing, Household or Student.  As long as the students each have their own invoice, then parents should be able to enroll one invoice and not the other in AutoPay.  If your school is utilizing household-based billing where both students are on the same invoice, AutoPay cannot be divided by child on one Invoice record.