Q. But the scholarship for $3500 does not cover tuition, it covered room and board for the summer.
A. The interview will ask how much of the scholarship was used for room and board. But, since the school classifies it as "scholarship", you are allowed to apply it to tuition, if you want to, to keep it from being taxable (not needed in your case). Be sure to "save" enough tuition to claim the tuition credit.
Q. The school added the $3500 for summer room and board(while he was doing the research) on top of the Box 5 amount if that makes sense.
A. Yes. That's common. All scholarship goes in box 5, not just the scholarship for tuition.
Q. The $6100 1099MISC is for the research stipend. I should not enter that amount in the 1099-MISC field?
A. Correct. Stipend income is earned income and you want it reported as such. TurboTax will enter a 1099-Misc as unearned income.
