Admins can mark tuition payments as paid if they receive the money in person and wish to do so.
SCP > Tuition Manager > Action dropdown > Manual Payment
Here you can choose an unpaid payment, and mark it as paid in full.
Under Payment Details you can select Cash or Check for your records, Type in an amount, and then pick whether you want the amount to be spread throughout all payments, or to be put towards the next payment, or in sequential order.