Q. I don't believe he owes any Federal Tax as his income is too low?
A. If his wages and taxable scholarship are less than $12,950, he is not required to file a tax return (nothing will be taxable). If he needs get any withholding refunded, he can file to do that, even though it's not required.
I, too, am not following what you mean by non qualified scholarship. If the "He was paid $6,000 for working on research" was reported in box 5 of the 1098-T, you have the option of applying it to tuition and other qualified expenses (books, fees, computer) and not declaring it taxable, depending on what works out best.
After entering the 1098-T, on the student's return, you will be asked if there was any scholarship not included in box 5 of the 1098-T. Enter there. Then you will be asked how much of the scholarship was used for room and board. Enter the amount you want/think is taxable there. Note the wording at that screen “or other expenses”. You didn’t have to literally use the scholarship for R&B.
