My opinion based on two different scenarios-(1)your company has pre-defined salary structure (2)You are going to define the slary structure for that particular employee.
In case of scenario (1) above- Your TDS amount will change accordingly elements of salary package.Beacause there is different taxation rules for allowances and perquisites.
In case of scenario(2) above- If you are expected to design the salary structure for that employee, I would suggest that you go through all of Income Tax Act and Rules regarding taxation of Salary so that salary elements designed in such a way that new joinee will be charged lesser amount of tax.
Hence TDS amount will vary on the different components of salary.
For your reference sending the link of websites which may help you to understand salary related taxation.
17 April 2012
U may put all tax free components in salary structure like Transport Allowance, Education Allowance, Meal Coupons, Medical Reimbursements, LTA, Telephone Reimbursements, etc.,