Dear Tejal,
You have not explained how many employees are working there. What is minimum and maximum salary structure (amount)? Whether you are covered under PF-ESI or not?
The proper hierarchy system can be formed by Grading System (Grade 1 to Grade 10, as per applicability). The Functional Designation can be integrated with the grades to maintain the hierarchy. (The supporting and general empl. (Upto 3 L CTC) can be given upto 4 Grade, like senior and qualified staff (upto CTC 5 L) can be given 5-7 Grade...... likewise).
Even the Grade can be linked with CTC as well.
The Salary structure in r/o lower grade (1-4) can be simple (Basic, DA (only if applicable), HRA, Conv, Medical Allowance, Spl Pay, PF-ESI (if applicable) etc.
However, in r/o higher salary structure the CTC can also modified to give them Tax Benefits (LTA, Tel./Petrol/Car Maintenance etc re-imbursement can be included in the CTC). Since the allowances are tax exempted against re-imbursement (pls check if there is any ceiling under the Income Tax Act). The LTA is tax free as per govt. notified rules (2 journeys are tax free in a 4 year block period).
Moreover, yours is a CA firm, I don’t think you need any advice from outside. You can get valuable advises from you internal source/s.
Pls work as per above, if you find any specific query share the same for further clarification/s. Fellow members can put more light on the matter.