You are liable to obtain PTR registration, deduct the PT from monthly salary of employees and remit it under the PTR obtained even though you have only one employee.
Strictly speaking, since you are operating from multi locations in Maharashtra, you have one employee in Mumbai and one in Pune, you need to have multi registrations (two registrations) under PTR. But, you can show the salary is paid from one place only. Accordingly you can have registration at one place and comply.
20th April 2014 From India , Mumbai