Hi Prasad,
Please specify your issue/requirement in time lines, so that we can understand the issue clearly).
Scenario (as understood by me):
1.Financial year 2015-16, Payroll was run month wise. April to September.
2. Voluntary Income tax was deducted month wise (approximately 20% of Gross salary)
3.Exemptions/Deductions were not maintained in SAP.
4 Challan mapping program is to be run for Sep.2015 (for II Quarter) and form-16 is to be generated.
As per the input given by you and my understanding:
1) Normally in SAP, you should capture the exemptions/deductions in infotypes for all the employees, so that, income tax is correctly calculated by SAP by using projection factor.
2) If employees have not declared the investments/tax exemptions so far (in our company, a common circular will be issued to submit the proposed amount by Dec/Jan Month and the actual amount by Feb month, so that correctness in tax calculation is achieved as well as negative salary in March is avoided), you can advise all the employees to give the proposed value. Else, you have to deduct income tax by entering voluntary tax (as mentioned by you).
3) You can run challan mapping and and submit quarterly returns. But, by March month, all the tax exemptions/deductions must be finalised and payroll should be run so that Form-16 will reflect the proper, section-wise tax deductions/exemptions.
Note: Even, at any month, employee's PF, Ptax, monthly LIC deductions can be used for calculating aggregate deductions/80c etc.
Please explain you scenario further, if I am wrong in understanding your issue.
regards,
Bala.