Its Simple, take deceleration in form 12BB, Calculate Income By Taking Salary you pay them and adding any perquisite you provide. This does not include contribution of Employer to PF as it is exempt. Deduct exempted portion of HRA, Transport allowance and other things. Then deduct employee professional tax actually paid. Then deduct all 80 C +80ccc+80CCD+80D+80DD+80G and many other Deductions employee has disclosed in form 12BB. When you have gross total income calculate Tax on the basis of Difference in gross total income and minimum exemption limit.
If you are not sure of what you are doing take help from an expert.
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