TurboTax will subtract the amount in box 2 (or box 1) of your 1098-T from the amount in box 5 and enter the result on line 7 of form 1040 with the SCH notation.
If that number is not the correct amount to be reported on line 7, add the additional amount at scholarships and grants in the follow up interview. It will take several screens to get there. The screen will be titled "Did YOUR NAME receive a scholarship or grant in 2016". The screen will already show the box 5 amount and give you another box to enter "Other scholarships/grants/fellowships". That will be followed by a screen where you can enter the amount not used for expenses.
