Setting up and using payroll software needs some training. We have tried to lay out the sections and articles which you need to go through and also the order of the articles to gain an understanding of the system in totality.

To gain an understanding of various aspects of payroll module please go through the following articles -
1. Scope of payroll - gain an understanding of the types of employees which are covered in payroll
2. Design of salary - what are the different components of salary structure and what are the tax implications
3. Understanding tax implications - refer to this article to understand the various types of tax free heads
4. Flexi pay / Flexible benefits - if you want to allow employees to design their own salary then this option needs to configured
5. Payment of Overtime - how to pay overtime to employees
6. Payment of Gratuity - details on payment of Gratuity
7. Payment of Bonus - managing payment as per Bonus act
8. National Pension Scheme - how to setup and use NPS option
9. Managing perquisites - some perks if given attract perquisite tax
10. Loans and Salary Advances - understand various types of loans / salary advance and their taxability
11. ESIC - managing deductions under Employee State Insurance rules
12. Multiple country payroll and changes in employee's location - if the employee is transferred from one location to another some cases his status changes from local to expat or even within a country there might be different laws at the state level

To understand how to setup the payroll module please go through the following articles
1. Payroll setup – this is the overview article which further gives the links to each section
2. Uploading year to date data - if payroll system is being initialized from middle of year then you will need to upload historical data

Activities to be done during payroll processing are covered in the articles given below -
1. Payroll process overview - This article summarizes and gives links to further articles explaining the activities needed to be done during the monthly payroll run
2. Payroll reimbursements – this process is use for claim reimbursements like Fuel, LTA etc. Employee can claim their amounts through the portal and upload supporting documents
3. Full and Final processing – this process is use for separation to employees which are working in organization
4. Quarter / Six month / Year end processing – some challans have to be submitted at the end of quarter, six months or year. These are created by the Payroll Manager as per requirement. The end of tax year processes include unclaimed reimbursements, net tax deductions, annual payments are managed and the setup for the next year is prepared
5. Tax Saving Declarations and Tax Saving Submissions – there are various components like House Rent, VPF, Tax Savings, Medical, LTA which can be used by the employees to save tax. Tax is calculated on declarations for the year till Jan / Feb period after which the employee is expected to submit proofs
6. Updating payment details - once payments are made to the Government the details need to be updated back in payroll module, these details are needed for subsequent generation of compliance documents
7. Managing Loans and Advances - loans can be given and an instalment deducted from monthly payroll. Loans can be with or without interest and can have perquisite tax linked to them