Even though you are operating from Mumbai as you have office across India under few acts you may have to maintain certain statutory registers based on the respective state.
As per Shops & Commercial Establishment act (Required separate registration in each and every states)
As you mentioned as you are following Online payments and all the records are online in few states you may have to take prior approval from from respective department concerned persons as well as in respective locations you may have to have all the registers such as Muster Role, Leave with wages register, extract on equal remuneration act, payment of gratuity act etc
You may have to have PT registration pertaining to particular location and the same amount has to be remitted to respective states for the employees
For example if 8 persons are working in Karnataka then you have to deduct for those 8 persons as per Karnataka PT act and have to remit to those department