It is not the 501(c)(3) status that dictates how the check is handled; it's the IRS rules on what constitutes taxable income, along with whether you want to increase the chances that the money is used to pay for tuition. Scholarship income is tax-free only if you are a candidate for a degree at an eligible educational institution, and it is not supposed to be used for certain things like room and board. If you make it payable to the school, then you know it will go towards something that they will pay for at school; otherwise, if you make it payable to the individual, they could just use it for a years worth of Starbucks (well, guess it depends how big the scholarship is). Any amounts paid to individuals in the form of scholarships are not required to be reported to the IRS by the payors, but it is less clear that it is a scholarship if it is written to the person instead of the school. (Fortunately, it's not your problem to figure out whether any part of your scholarship is taxable to the recipient.)
See here for more info: http://www.irs.gov/publications/p970/ch01.html
I guess I'm wondering why you wouldn't want to make it payable to the school. Rose's suggestion to get a receipt that it was used for the intended purposes would work, but given that the recipient really has no motivation to give you that receipt, and it likely won't come for months after your books close, I'm not sure how practical it is.
Our PTO awards scholarships at graduation night. But, they are not paid out until the following January after the students submit schedules for 2nd semester at school, along with their transcripts from 1st semester at school. The checks are made payable to the student. If a student does not return to school for 2nd semester, they do not receive the scholarship. If that student returns to school the following year and submits transcript and schedule, then the scholarship will be paid out at that time. The student can use the award for whatever is needed. (tuition, books...)