Your employer does not have to include the tuition reimbursement in your pay stub. This is as long as you are not a highly compensated employee (meaning a 5% owner or earned $120,000 in the previous year). See IRS guidance: https://www.irs.gov/pub/irs-pdf/p15b.pdf
You will need to enter the employer reimbursement in TurboTax under the Education Summary section, select Scholarship and Grant, Employer Assistance is on the next page. This will adjust your education credit.
It will not affect your 1098-T. That comes from your school and does not take into account employer educational assistance.
Your employer can use the tuition reimbursement as a business deduction up to $5,250. Over that amount it must be included in your wages.
[Edited 01/17/18 | 6:18 pm]