Dear Nikhil,
The deduction of PF-ESI is subject to registration with the dept. If the No. of employees in your organization has reached to the minimum no., as specified in the acts, than you have to apply for the registrations immediately and deductions should be made accordingly.
However, if you are doing on voluntary basis than it can be done as per your preferences. Before deductions started, you have to define the salary structure in such way to maximize in hand salary with lower statutory cost to company and lower Income Tax deduction (TDS). There are different criteria (depend upon the CTC level, no. of empl., Industry etc.) to define the salary structure as per requirement.
However, if you are legally not bound for the registration, than the gross salary & net salary (in hand) will be same.
Fellow members can put more light on the matter.