The deposit might not necessarily be for the same school as the NCP forms. If, as I suggested above, your son has just received a call from a waitlist – it could be that either he wanted deposit money for School A before hearing about the waitlist spot at School B; or that he wants deposit money to hold a spot at School A while waiting to hear about financial aid at School B. (The timing of the two requests would tell you the answer)
Students are not supposed to double-deposit, but coming off of waitlists is an exception to that rule. Under the possible scenario that I describe above, then it might actually be a smart thing to deposit by May 1 at School A if still waiting on a financial award from School B.
In any case, you can simply tell your son that you will make the deposit directly for him online and ask him for the link to the college web site and whatever info would be needed to make the payment (such as account or student ID number). You would know when you got to the website which college it is.