Did you figure this out? I am in the same situation as your son where I was issued a W-2 which I filled out covering Jan-Sept but Sept-Dec I was covered by a fellowship and received 1098 T and nothing else for that time. My Box 5 on this is higher than my box 4 by $857 so I think that I only have to pay taxes on this difference. I paid my estimate taxes already via the IRS payment system, so I am confused at where to enter this payment.
