"My tuition reimbursement was not taxed but it was included in my gross income on my W-2".
Those two statements are contradictory. All money in box 1 of your W-2 is (or will be) "taxed", because it goes on your form 1040 as income. I assume you mean there was no withholding done for that amount.
You are not allowed to deduct $5250. If $5250 of tax free money was included in box1, of your W-2, you need to ask your employer for a corrected W-2.
Q. Or would I just enter the 1098-T form in the education section and not notate any employee reimbursements since the $5250 was added to my gross pay in my W-2?
A. Maybe. Yes, if none of the employer reimbursement was tax free. But, first verify with your employer that $5250 is supposed to be tax free. Not all employer plans qualify for tax free treatment (most do). If it does qualify, a corrected W-2 is the only remedy.
