Tds applicability

i am accountant in Pvt Ltd company. In the said company some  salaried emloyees will cross taxable limit for F.Y.2016-17 and some are below taxable limit. So how company should deal with these employees in accordance with TDS. In TDS return for March ended 17 should I show only taxxable employees for whom company is going to deduct tax from salary. If an employee is above taxable limit but he provides valid proofs of elgible deductions thebn also we have t oshow this in TDS return because after showing deductions taxable income is NIL. What are other points to keep in mind while filling TDS return for Salary!